Legion was fine. Geth were never pure evil, and even the first game hinted that both the geth and AIs in general had more to them than killing all organic life. The examples that come to mind are the random side quest where the geth were listening to some quarian opera, and the newly created AI on the moon begging for help when you shut it down. It's not much, sure, but it was pretty obvious that they were breadcrumbs meant to lead somewhere in the sequels.
The prothean was just insultingly stupid. Bringing one back at all was a mistake, but it could have worked somewhat if it was a wise old guy that could have told you lots about their history and civilization. But no, they retconned him into some bug man specifically because they thought it would be cooler. Absolutely idiotic, and like everything in the sequels it felt like a deliberate attempt to tear down the legacy of the first game. Speaking of which, I recently remembered that they gave you a fucking hard light Assassin's Creed wrist blade. Not only does it look stupid, it makes no sense with the way hard light works in the universe. You either wear special gloves that create the illusion of being able to touch the holograms, or if you're a true hackerman you can go through an operation that implants the tech in your fingers. Simple and sensible sci-fi. Then ME3 came along with its stabby wrist blade.