Honestly, the biggest problem is removing the Virmire Survivor in ME2. Even if you played MShep romancing Ashley, it fucks you over.

And most of the characters they added in ME2 were garbage. I would argue that even when they were well-written, they were still unnecessary, and just watered down the development of existing characters.

Obviously, this is a huge impact to gay players, though, as Kaidan is all we get.