Please note that I'm not a commited Marvel reader, I read the news stories, watch the movies, watch the TV shows and I only started buying mainstream Marvel comics again at the start of the Spider men event so please forgive me if I miss any obvious changes.
Captain America has 2D wings on his helmet and now has visible shoulder pads on the outside of his costume. He has lines on his suit similar to the ones on the current Superman and Batman suits. Please note: Cap is not carrying a gun but there is a bit of poor positioning with Nick Fury's hand which makes it look like he is.
Nick fury is now the Ultimate universe or Cinematic universe version of Nick Fury, I'm aware that this character has already been introduced into the 616 universe but I don't think he's been confirmed as a main character yet and it looks like he'll have a big part in the future of the Marvel universe.
I think Nova has a slightly diffeferent logo and helmet.
Jean Grey is now returning to the Marvel universe, in her original X-men costume.
The Hulk is now wearing silver body armour instead of just purple shorts, he also has shorter hair than he usually has.
Spider man is now wearing a black and red costume rather than a blue and red costume. You can also see his eyes through his mask.
Thor now has a darker costume, has no cape, carries two swords on his back and now has blank eyes. He also has brown leather on his lower half.
Iron man has black and gold armour as opposed to his classic red and gold suit, he has red arc light all over his suit and he has red eyes.
I can't see any physical changes to Wolverine.
Cyclops now has a X shaped visor for his eye beams to come out of, he may have a dark red suit but this may just be reflecting from the light in his eyes.
Sue Storm has a white suit with shiny black lines on it.
Who I think is cable now has a black eyepatch and a red bodysuit, he is no longer carrying guns on his back.
There is also a floating S.H.I.E.L.D. robot and the reflections on it's visor make a sort of face.
Feel free to point out any mistakes I didn't notice.