Wow! Lots of opinions on this topic. Many valid, some vague, some completely off topic. I'll toss in my two cents worth.
1) Batman: It has long been established in the comics that Batman wears body armour under his tights. Even before Dark Knight Returns. Back in, I think it was the sixties, there was an issue of Batman where on the cover The Joker is shooting at Batman as Batman is charging at him and shouting "Why won't you die?". In Batman's thoughts he's saying "Hasn't Joker ever heard of a bullet proof vest?". Now the comics depict Batman as wearing spandex or spandex-like material over a well muscled and chiseled torso. Problem is, body armour doesn't allow you to show off your physique. It's big and bulky. So in putting Batman in body armour for the movies, it makes sense to make his body armour be designed to look like a muscular torso to keep that "iconic look". I will say, however, that I never liked his cowl being that restricting. I used to be a pro wrestler, and I wrestled under a mask. Even the best designed luchadore masks hamper you periferal vision to some degree. The ability to compensate by turning your head is vital for your own safety.
2) Captain America: Being Canadian, I don't follow Cap quite as much as I do other heroes. However, I do agree that his costume should be as close to the comics as possible, as he is a superhero icon. However I also agree that his costume should be explained in some sensible fashion. I haven't seen or read anything on the "USO storyline" you all keep harping on, but I will point out a few past stories that address the issue. In the recent animated film "Ultimate Avengers", during WWII Cap wore a uniform more "military" in design but still with many of the classic elements of his more iconic costume. Then after he's found and revived he's given a new "updated" costume by S.H.I.E.L.D. That's one way to go with the live action movie. Now in the live action Captain America movie that came out in the 1980s, his uniform and shield were designed by the scientist who created the Super Soldier formula that made both Captain America and, in an earlier test, The Red Skull. They were made out of a special materian that was virtually indestructable. Captain America even made a comment on the bright colours, that the doctor "had very little concept of camoflage" or something to that effect. And another soldier replied with something like "she did love the red, white, and blue". Either explanation could work here, or even a combination of the two.
3) Other Comic Book Characters: Most of the other superhero costumes that've come out lately have looked very much like the original comic book designs. Spiderman, Fantastic Four, Dare Devil, Spawn, Ghost Rider, Hellboy are all great examples. Not all of them were great movies. I mean, Jessica Alba isn't my first pick for Sue Richards. But you gotta admit, she looked great in those blue tights. Seriously, who wouldn't want to take her, bend her over, and make her squeal like a pig?
As for all the costumes that look nothing like their comic book origins. Honesly, would you really have taken Bullseye seriously as a villain if he showed up wearing blue and white spandex with a target printed in the forhead of his mask? And Elektra? In the comics she fights in a one piece swimsuit with a neckline that plunges down to her navel and a back that rides up her but! Can you picture Jennifer Garner wearing something like that? Let me rephrase. Can you imagine her fighting in something like that without realistcally having a wardrobe malfunction halfway through the fight? And let's face it, The X-Men in matching black uniforms looked so much better than them all wearing yellow and blue spandex (although I wouldn't mind seeing Halle Berry in the white bikini and knee high boots that Storm used to wear back in the day).