Ok, being an active reader of ALL Ultimate titles, here's my take on those choices and how I feel:
Iron Man: a human brain: Ok, I admit it. this is crap. It makes no sense, and thinking about it disgusts me. When I read the Ultimates, I don't even think about it.
Wasp: Mutant: This I almost saw coming. It just makes more sense to me. And really, who cares? Wasp is cool, she has powers, she kicks ***. Does it really matter how she has her powers? Not really.
Thor: looney liberal: I love this take on Thor. Much more interesting and believable. He just seems more....human to me than 616 Thor, and tat's a good thing.
Scarlet Witch and Quick Silver: Apparent incest: Love it. I always looked at their relationship in 616 and thought it would be more fun and interesting if they had that whole 'touchy touchy' aspect to them. I don't think it's incest, but it seems that way to everyone else, making it very fun to watch.
Ultimate Reserves: Considering that the Ultimate's are an actual Government ran super team, it makes sense that their would be reserves. And come on, there were reserve Avengers in 616, so why not here?
Captian France: He exists: Ok, gotta give you that. Captain Britain was bad enough, at least he exists in 616, but Captain France? WTF?
Defenders: No powers: Eh, I never liked the 616 Defenders, so I don't really care.
Venom and Carnage: created in a lab: I am personally a huge fan of the Ultimate Symbiotes origins. I always hated the whole alien aspect of it. Having them as man-made creations seems much more realistic to me. The only problem I had is that while Venom still felt like Venom to me, Carnage was not Carnage. At least Eddie Brock was in the Venom Suit, but no Cassidy? Cletus Cassidy made Carnage Carnage. Without Cassidy, Carnage was just crap.
Dr. Doom: Skin is metal: Ok, I was a fan of the movie, and I thought metallic skin instead of body armor was a very cool twist on an awsome villain. Although I thought the hooved legs were a little much, I thought Ultimate Dr. Doom was very well done. Can't wait for him to return.
Green and Hobgoblin: actual goblins: This is the Ultimization I love the most. The goblin costumes were getting really old to me in 616. So making them actual Goblin monsters was just an awsome idea. They seem so much more terrifying than their 616 counterparts. So I applaud this one.
Black Cat: hair is black and wears white wig: Dude, who cares. Wig or not, Ultimate BC rules! And if possible, I think she looks way hotter and sexier than 616 BC. So I don't care if it's a wig, considering it's not to much of a stretch to think of the wig as another means to conceal her identity.
Skrulls: Chitauri: Yeah, their name is different, but they are so much cooler. 616 Skrulls were so cheesy, the Ultimate Chitauri are not. Next?!
Daredevil: doesn't show up often enough: Yeah, because he's the same as 616 Daredevil. Nothing's different, so he has become stale. Now Moon Knight on the other hand rules in Ultimate. So screw Daredevil, I want more Moon Knight!
Colossus: he's gay: Heh, this one kinda made me laugh. But really, I'd rather complain about Beast being killed off than weither Colossus likes boys.
Xavier: What about him? He's cooler, deeper, more manipulative in Ultimate than 616? Because if that's what it means, you're right.
Phoenix: American diety: This one is ok, but I'm a little used to seeing Pheonix laying waste to solar systems, so I gotta let this one grow on me for a while.
Emma Frost: pacifist: This is one of my favorites. I kinda like seeing Ms. Frost so much more mature and peaceful. It increases the mystery about her and makes me wanna see her fight that much more.
Spider-Man & Shadow Cat: dating: Easily the best Ultimization of them all. I always thought Ultimate Kitty Pryde and Peter Parker would be perfect for each other. Kitty is a much cooler and more interesting character than Mary Jane, and it opens up a lot of Spidey/X-Men team up possibilities.
Plus, Ultimate Kitty is way more attractive than MJ. You go Pete!