1) Different environments - there's no feeling of progression, unlike the past three games (especially MGS3), where you felt like you were indeed sneaking further and further into an enemy stronghold.
Also given no chance to really connect with the locations. Just as you're really getting into each environment, you're suddenly shuttled off to somewhere else in the world.
2) Codec got neutered - only two people to speak to, and one of them just repeats the same useless rubbish each time you call her. (Really: we have an entire bar in the corner of the screen to tell us how stressed Snake is, why do we need someone to also tell us?)
The codec was actually one of my favourite thing in the old games. I loved just stopping and calling up my support group every now and then, just to see what they had to say. Only really having Otacon to talk too (who took on Colonel Cambell's and Major Zero's boring roles - telling the player where to go next) was dissapointing.
3) Cutscenes to gameplay ratio all over the place - sometimes it felt like you'd barely been playing much before yet another lengthy cutscene started. I think of all four MGS games, MGS3 got the gameplay to cutscene ratio the best.
4) Too many gunz/aquirement of gunz - loads of guns, but there's not really much point in buying most of them.
Not only that, but having these guns readily available to buy also meant the game lost yet more of the feeling of progression that past games had. In MGS1-3, when you found a new gun it was always an exciting moment. MGS4 lost that feeling.
