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Crowley is Lucifer and Aziraphale is on his way to become Archangel Raphael. Let me explain.
First, for reference, here are the classes of angels:
Highest Orders (Archangels)*
• Seraphim
• Cherubim
• Thrones
Middle Orders
• Dominions
• Virtues
• Powers
Lowest Orders
• Principalities
• archangels*
• Angels
*It is important to note that in this context, an Archangel and an archangel are very different entities. Neil Gaiman has clarified that this is a canon distinction; capital-A Archangels are any high ranking angels while lowercase-a archangels are lower ranking angels.
In Good Omens, there are 3 angels that are explicitly referred to as Archangels: Gabriel, Michael, and Uriel. Now, there are a variety of different interpretations of the Bible and who the correct group of Archangels is, but generally the main 4 are considered to be Gabriel, Michael, Uriel, and Raphael. In addition, Lucifer was most likely part of that group as an Archangel before he Fell, as he was once God's favorite.
So, that means there are 5 Archangels in total, but only 3 have made appearances in the show so far. Lucifer does not count, because it is important to note that in the original Hebrew Bible, Lucifer and Satan are separate entities. That is most likely the case for Good Omens, as they always say "Satan" rather than "Lucifer." This is intentional because Crowley is Lucifer.
It is basically confirmed at this point that Crowley used to be an Archangel before he Fell. This is heavily implied twice in Season 2. First, whenever he is talking to Shax about the miracle he and Aziraphale performed together, and she says that it only could've been accomplished by an Archangel. Crowley's response is "how do you know it wasn't me?" and then they carry on with conversation as though it was a joke. But Neil Gaiman is a very intentional writer, and I don't believe he would write a line like this only for it to go nowhere.
Besides, he later all but confirms Crowley's status as a former Archangel when Crowley goes to Heaven with Muriel. They tell him that Gabriel's file can only be accessed by someone of high status, and Crowley flips it open like it's nothing. Crowley is also just generally shown to be an extremely powerful demon, so it can be assumed that this is because he was an extremely powerful angel.
So, Crowley was an Archangel, but the big question is which one -- Raphael or Lucifer?
The theory that Crowley is Raphael has been popular on the internet for quite some time now and while there are some valid arguments, it's unlikely. Neil Gaiman was even asked about this theory on Tumblr, and while he didn't outright deny it, he implied that it was untrue but still a cool idea nonetheless. The odds that he changed his mind since then are low, and even if he was inspired by it, making a theory canon just because it became popular doesn't seem his style. It's much too predictable, and Neil Gaiman is anything but predictable.
Not to mention, Crowley being Raphael doesn't make much sense considering the fact that Raphael doesn't Fall. Though Raphael isn't mentioned much in the Bible, he does make some appearances and is known as an Archangel who spends most of his time as a healer among humankind. Crowley, on the other hand, Fell before Adam and Eve left the Garden of Eden. Sure, some creative liberties could have been taken and obviously the Bible is only inspiration for Good Omens, but it's doubtful that Neil would change this much biblical lore, especially since Lucifer is right there as another option for Crowley's Archangel identity and it fits perfectly.
There are a lot of hints in the text that point to this theory, but here is a list of the major ones: (this will be updated and added to)
1. Lucifer also goes by the names "Morningstar" and "Light Bringer," respectively. In the first scene of Season 2, Crowley is seen as an angel creating stars and says the line "let there be light."
2. As mentioned previously, Lucifer was also God's favorite angel. This would make sense considering Crowley seems to know quite a bit about the inner workings of Heaven, God's Plan, and even sometimes talks to God out loud as though he's spoken with her before.* Crowley also seems like the type of character who wouldn't want to use that favoritism for personal gain, which would explain why he blatantly avoided introducing himself to Aziraphale when they first meet as angels.
*There are a lot of examples of these occurrences that other people have pointed out, but they're very specific lines from throughout the show and I don't have the energy to find them all right now, but I will update eventually or you can find them on your own.
3. Crowley insists multiple times that he didn't mean to Fall and that he only became a demon for "asking questions." This sounds an awful lot like Lucifer, who is often portrayed as pure evil but who was really just an angel who lost faith. Crowley questioned too much of God's plan and refused to conform to the rules of Heaven, so he was cast down and seen as a monster. This would explain why Crowley resents Heaven so much and why he stands apart from the other demons. Him being Lucifer would add such an interesting layer of depth to the morality conflicts and nuanced character arc that he already has.
4. It is already a known fact that demons don't keep their angel names when they Fall. That is the whole reason for the debate over Crowley's angel name, so it's contradictory to assume that Lucifer in Heaven would also be Lucifer in Hell. There's no reason he couldn't have changed his name, especially since Crowley originally came from Crawly, the snake who tempted Eve.
5. And that's another thing -- Crowley was canonically the one to tempt Eve in the Garden of Eden. In the Bible, that act is often assumed to have been done by Lucifer. Lucifer is also associated with snakes, same as Crowley.
6. There are some other actions that Crowley makes in the show that Lucifer makes in the Bible. For example, Crowley hints at meeting Jesus and "showing him the kingdoms of the world" and Lucifer tempted Jesus in the desert. Also, Crowley is sent to reign down destruction on Job, a task often attributed to Lucifer.
7. It is likely that Lucifer knows Gabriel from when they were Archangels together, and that is part of the reason he hates him so much. Whether or not Gabriel remembers Crowley or that he's Lucifer is debatable, but it is strongly hinted at that Gabriel and Lucifer were both Supreme Archangels at one point (either together or Gabriel succeeded Lucifer). When he is being fired, Gabriel and the other Archangels comment that they can't send him to Hell because that would be a repeat of another Supreme Archangel. That Archangel in question is undoubtably Lucifer, and the camera focuses on Crowley when they say that, implying that they might be the same.
8. In the heartbreaking Season 2 finale, Aziraphale tells Crowley that he "doesn't understand what he's offering him." Crowley responds by saying that he not only does he understand, but he probably understands better than Aziraphale does. This is because he has had the position of Supreme Archangel before and it went poorly. Crowley's furious reaction to hearing that Aziraphale was offered the job is not just because he hates Heaven and loves Aziraphale, it's because he's been in Aziraphale's place and he knows that it's a trap but he can't stop him. He is also angry that Aziraphale thinks he wants to go back to Heaven, because he knows that he would not be welcomed back as Lucifer, nor would he want to be.
9. Metatron acts as though he might know Crowley. When he and Aziraphale leave on their walk, he turns to give Crowley an evil look and sinister music can be heard. Crowley also seems very distraught while waiting for their return. Metatron is the Voice of God, and Lucifer was God's favorite, so it makes sense that Metatron is the only one aware of Crowley's identity and that is why he wants to separate him from Aziraphale. Cutting off someone's support system is a classic manipulation tactic, and Metatron knows that Aziraphale won't come back to Heaven if he's still attached to Crowley. Notice how Metatron is ths one who suggests Aziraphale restore Crowley to angelic status -- knowing full well how upset Crowley will be at the idea of being Lucifer again. Metatron is a master manipulator who knows Crowley's secret and won't hesitate to use it against him.
Those are all the main reasons that come to mind when justifying the Crowley = Lucifer theory. There are only 2 arguments that would make sense to be used again it, and neither of them are very strong. There is a line in Season 1 where Crowley mentions that he "hung out with Lucifer and the guys" but that could easily be read as him talking to himself in third person. Or it could be a small retcon and that would be fine, seeing as the story was not originally meant to continue and most (if not all) of the content past Season 1 was not planned ahead of time.
There is also no explanation for why no one seems to recognise Crowley as Lucifer and why he hasn't told Aziraphale, but these could be very easily explained if/when Crowley reveals his identity. There are many potential reasons for keeping that detail a secret, and if this theory is true, there will be a plot twist in Season 3 to reveal them.
Now that Crowley is more or less established as Lucifer, let's move on to why Aziraphale will become the Archangel Raphael in season 3.
First, there has to be a reason as to why Raphael is noticeably absent from the council of Archangels in the show. In the Bible, Raphael isn't mentioned much but he is portrayed in various interpretations as being a healer, helper of travellers, friend to mankind, and holding a staff with a snake. These traits all make sense for Aziraphale -- he helps people, guides them, loves humanity, and is often accompanied by Crowley, a snake. I have also seen it mentioned that Raphael's physical description and personality match Aziraphale's, though I'm not entirely certain how accurate that is.
At the end of season 2 , Aziraphale is promoted from Principality to Supreme Archangel, which explains why there wasn't a Raphael before, but there will be soon. Raphael is known as Israfil in some translations, and he goes by the name "Azariah" when pretending to be a human in the Book of Tobit. Both of these names sound very similar to Aziraphale. Similarly, the end of Aziraphale's name sounds like Raphael. "Azi-raphael." It would make sense for him to be renamed to signify his new return to Heaven and his new position, and Aziraphale becoming Raphael would complete the 5 main Archangels at last.
Now that we've gotten all those technicalities out of the way, how could this theory play into Season 3?
In my professional opinion, Season 3 will most likely begin with a time skip. Neil has said that Season 3 comes from ideas he planned out with Terry Pratchett, and that Season 2 was simply a bridge to connect those stories together. Season 3 will begin with Aziraphale -- now Supreme Archangel Raphael -- presiding over Heaven and aiding the Second Coming the Metatron hinted at. This is where the name change is important, as it will be one that Crowley is not anticipating and will add more fire to the betrayal he feels.
It is naive to believe that Aziraphale will notice the flaws in Heaven immediately. The religious indoctrination that he has suffered is too intense to be undone so quickly, and though it hurts, he will most likely spend a lot of time in Heaven trying and failing to make improvements before he realizes that Crowley was right about its toxicity.
What people (especially those who believe in the coffee theory -- sorry) don't seem to understand is that Aziraphale is in an extremely abusive relationship with Heaven and is still a ways away from breaking out of that cycle. There are a million TikToks and other analyses out there that explain Aziraphale's motivation for returning to Heaven, but it's not a decision that Neil will undo immediately when it has so much potential. It is also not one that will be dismissed with the excuse of "oh the coffee was poisoned and he was brainwashed." That is a cop-out and it is lazy writing. Neil Gaiman is not lazy. He is absolutely 100% going to milk that angst for as long as he can, as unfortunate as that is for us to hear.
This next part of this theory is a little bit of a wild guess, but I have a feeling that Season 3 will revolve around Heaven's second attempt at an apocalypse, which will end up being all of humanity vs all of Heaven and Hell combined. Crowley hints at this concept at the end of Season 1. Here is the exact dialogue:
Crowley: If you ask me, both sides are going to use this as breathing space before the big one.
Aziraphale: I thought that was the big one?
Crowley: No, for my money, the really big one is all of us vs all of them.
Aziraphale: What? Heaven and Hell against humanity?
... and then Crowley changes the subject. Once again, a perfect example of him appearing to know "ineffable" details about the future without explanation. Him being Lucifer and revealing this information in Season 3 would be a huge shock, and it would combat the betrayal of Aziraphale becoming Raphael.
In addition, these roles place Crowley and Aziraphale on opposite sides of the apocalypse once more. Crowley on the side of humanity, and Aziraphale on the side of Heaven, who will end up working with Hell to assure that the apocalypse goes correctly this time. This will spark a lot of conflict, self reflection, and growth for our 2 leads.
Aziraphale will get the opportunity to complete his character arc and fully separate himself from Heaven, ending the manipulative and toxic hold it has always had over him. Crowley will most likely have some sort of reconciliation or conversation with God (I am quite certain God will make an actual appearance in the finale of Season 3). Both of them will finally get to be together and mend their relationship properly, without being influenced by the notion of sides. Finally, there will truly be an "our side" -- and it will include the rest of humanity as well. I'm not sure how Neil will wrap the story up from there, but I have faith that it will be very satisfying.