MGS3 for me.
Passing, Gameplay, story, boss fights all are great.
RE4 is more of a really good visual treat. If you are to actually look past the great set peices from one area to the other you'll realize its pretty shallow.
The puzzles seem like they were made for 10 years old to solve not only that but it's basic action horror game puzzles. It's like they took Leon out of RE and put him in gothic type castles or whatnot of DMC with more bullets and zombies.
Now that sounds great fun but it kind of got boring for me 9 hours into the game. Im not even att he second disk yet.
The story is.....well.........different. This is where the game falls the most. After going through rooms and rooms of zombies and puzzles for nearly 3 hours straight I want some story to grab me back into the game, so I will go through 3 more hours of same bullshit over and over again.But the story doesnot do that at all. The characters are annoying to say the least, the voice acting horendous. The cutscenes are well directed, but they try too hard sometimes(the scene with ada and leon.

)
Other than the camera, which doesnt annoy me much, I think MGS3 is one of the finest and most perfect games ever made. The pacing is just like a movie, it grabs you and the gameplay so awesome, you'll want to play same areas over and over again just because it's so different every time. While in RE4 the difference is in the envrionments and set peices rather than what you're doing.
RE4 is a must buy game, but I just think people are kind of overrating it a bit . Look past all the nice castles and ligthing. FOr a action game IT is suppose to grab you with its visuals but Gameplay in MGS3 is far better, more open eneded and varied than anything in RE4.
Both are must buy, But MGS3 wins this one.