I just finished the game and I'm still undecided. There were a lot of things I didn't like but I can't say that it was a bad game. MGS3, although far from perfect, still remains my favorite game in the series.
Some random things I didn't like that come to mind:
1. Cheese. Now, I know that the series are sort of known for it but they have always done it with a sense of humor. No matter how cheesy things got, they never failed to make me laugh; MGS4 on the other hand, made me cringe, constantly.
2. Cutscenes. This is sort of related. The cutscenes have mostly been entertaining in the series, while in MGS4 they drag on and on with pointless crap that the game could do without. Those Mission Briefings got unbearable on several occasions for me. I honestly fell asleep during one.
3. Characters. There are no cool characters here, especially compared to something like MGS3. Every old MGS character that's still alive makes an appearance and some of them are there just for the sake of being there. All the new characters are plain boring.
4. Enemies. The B&B's are ok and I get the reference to the old bosses but they're all lame versions of the old ones. On top of that, the old bosses usually participated in the story in some ways. In MGS4 they just pop up to give you a boss battle and then you get an extremely corny story that tries to create an excuse for them being there. It almost feels like they're an afterthought.
5. Codec. I'm really disappointed with this area. Kojima had fun with the codec, in previous games. Remember MGS2? It felt as if the NPC's knew what you were doing at all times and had minds of their own. Here, we get pretty much just one person to talk to (rosemary repeats the same useless crap over and over), and they never say anything interesting.
6. Gameplay. I'm not talking about controlls or anything, that area has never been better. It just doesn't feel like a stealth game anymore. I must have killed hundreds of people, without trying. It's like a freaking action game now. I can't imagine playing this without any kills.
The good:
1. Guns. I love how they handled the guns in the game. There is a crap load of them and they all feel awesome. Every pistol feels unique and lethal at the same time. It seems like that part was done by a real gun lover.
2. Finale. The ending was spectacular, as expected. The whole game got a lot better toward the end, now that I think about it.
3. Story. The story got too messy and confusing back in MGS2 but I do like that MGS4 left no loose ends. Too many sequels (both movies and games) choose to leave things unanswered, and raise new questions instead. I like that effort, although honestly the MGS2 - MGS4 story is out of control.
Overall, it's definitely not the best game in the series but it's still digesting so I don't know if it's the worst yet.