As someone who went into D&D from videogames (FF II/IV, if you must know)...
I don't see whats "wrong" but I'll tell you what others seem to think...
1.) Perfect character combinations. X classes + Y feats = invinicible. New feats/prcs/spells are designed to make your pc uber. Not necessarily munchkin, but uber and unbreakable.
2.) Very Linear plot. A leads to B leads to C. Railroaded epic plots that usually revolves around getting powerful, kicking a bad guys ass, and saving the world.
3.) Emphasis on Equipment. PCs have suites of constantly upgrading items. Have a +1 sword? Look for a +2. Can't find one? Buy it! Can't buy it? take a feat and make it yourself...
4.) Unkillable PCs. Ressurection and other status removing spells make the PCs unkillable. They don't worry about death, they can "respawn" with a slight penalty (-1 level). Disease, poison, blindness, even lost limbs are temporary setbacks, not cripplings.
5.) EQ lingo. Everquest and other MMORPGs has given us such wonderful terms as tanking, pulling, training, buffs, bossfight, and farming, some of which have leaked into RPG discussion.
6.) Non-Medieval: Much of the art of 3.X is based on a concept of unrealisitic armor and clothing, non-medieval grooming, gnomes and halflings that look cool and adventuresome, non-believable weapons, and "kewl" looking monsters. The idea is to make it look cool, not believable.
7.) Occidental/Oriental: Western and Eastern concepts are mixed with little or no thought as to development. Monks and samurai wander with paladins and druids.
8.) Over the Top: The fights are larger, the spells grander, the gear spiker, and the damsels hotter. Everything is on a larger and more heroic scale.
9.) Magic is downright common. There is no real awe or mystery, just a cool factor for bigger and badder spells. Magic is sold in shops on the street. Clerics stand in temples to heal wounds and raise dead.
Personally, I don't see the problem. However, some people who would rather D&D be more Tolkien/Howard/Lieber and classical fantasy balk at the change in tone to the Final Fantasy/Everquest/Warcraft styles.