There has been something wrong with Aziraphale since s2, but I was only able to put my finger on it now after the show's ending. Aziraphale was Terry Pratchett's character while Crowley was Gaiman's. I relate to Aziraphale in s1. I feel like I can understand him on a deep, personal level. But since s2, the mannerism is the same, but something is off.
Aziraphale as I understand him would not abandon his bookshop for years without finding a way to (sneakily, if needed) check on it and make sure all is well with it. Doubly so for Crowley. If he went to Heaven to help organize the Second coming (if he even trusted Heaven - they tried to burn him with hellfire!), he would find a way to involve Crowley without Crowley having to become an angel. They're on their own side, after all. Even if he was threatened (the popular "coffee theory"), he would find a way to comply with Heaven outwardly while staying on their own side - he has millenia of practice.
But that's not the Aziraphale we see in s2 and s3. Why? Because he's no longer Terry Pratchett's Aziraphale. Gaiman sees himself as Crowley, so he felt the need to make Crowley the one who's right, who loves the world more, who is better, and who was wronged. Retrospectively, it's visible from the very 1st scene of s2. It's the reversal of their roles. Before, it was Cowley who was besotted with Aziraphale since the first meeting when he got a glimpse of his true self. Now the roles are reversed. It's Aziraphale who admired Crowley since first meeting him as an angel. And all through s2 and s3, up until the very end, he still admires the angel without fully accepting the demon. This is not the Aziraphale I know.
And Crowley is different, too. Suddenly he is the one who would sacrifice everything for the world, while in s1, he didn't care for the world without Aziraphale in it. It was Aziraphale who was willing to do anything to save it. But Gaiman wanted Crowley to be more, as if loving Aziraphale so fully was not enough.
Maybe he does not understand loving someone as fully. Maybe he only understands how good it feels to be important. In s2, it wasn't as evident, and it could still be interpreted differently, but it is evident in s3. Gaiman did not want to honor his friend's memory, he wanted to be important, and in turn, he wanted Crowley to be important and outshine Aziraphale.
s3 did a good job of closing the story with the characters and setting it inherited from s2. But now it's evident that the characters are not the ones from s1, it's Gaiman's twisted version of them. And that's ok, people can have a different interpretation of the same character, and for some people it will fit their interpretation. I do not claim that my interpretation is better, but I don't have to accept the one in s2 and 3, either. Sir Terry's Aziraphale is the one I identify with, not Gaiman's.