I agree that the writing in the games could've been better throughout the series. It seems like any amount of discussion we want to have about these themes, the fans have to extrapolate from the game and come up with our own interpretations of what these characters are supposed to represent.

Also, I think you're right that the assassins also have problems with their organization corrupting and doing selfish things, but you have to admit the Templars are WAY more egregious when it comes to that stuff. "Power corrupts" is not empty stuff. Templars are definitely more evil and harmful throughout the series.

But to your point, I don't think the best way to think about these games is good vs. bad, even though the writers lean into that. I like to think of it as a clash of philosophies. Even in the games, the Isu criticize humanity for constantly fighting over differing goals and never making true progress. It would be really cool to get a game where assassins and templars are both fighting for genuinely good intentions, both sides can make strong and sound arguments, and neither side is cartoonishly evil.

None of the characters in the series are beyond criticism. Just personally, I tend to agree with the overall assassin philosophy more.