Oh yeah, that was pretty horrible, but the X-Men book I'm talking about is the post-Ultimatum one, in particular the Brian Wood run. They mostly ignore the whole "mutants are a super soldier experiment byproduct" thing, although it is mentioned occasionally. The book is also pretty unconnected from the one your talking about, partly because Ultimatum killed off most of the X-Men... It's basically about a few X-Men survivors and new characters going from being hunted down by the goverment, hiding and being forced into camps to creating their own state and how that state interacts with the US and the other nation on Earth that explicitely welcomes mutants. And it was Nightcrawler who they made homophobic, while Colossus was gay.
Agreed on most of the Ultimates, although I did enjoy how the team mostly fought threads that arose due to its own existance or its members. And as far as 1940s Captain America goes, I was generally okay with him being a terrible person (the other characters I found pretty unlikable too), but at least during Ultimates 1 and 2 it felt like we weren't supposed to support the existance of the team or see Captain America as a super great guy. I have more of a problem with the later stuff that portrays him as heroic. Also, yeah the incest and cannibalism stuff is obviously horrible.