RE4 better than MGS3?? You HAVE to be kidding. It´s incredibly overrated, yeah, it´s a great game, almost a 9/10 IMO but come on, you have to be retarded if you can´t tell how freaking disjointed this game is.
I haven´t played it in a while, but IIRC most of the progression doesn´t make sense. In terms of environment, there really isn´t much reason why you access to the different areas, it felt more like Capcom mixed the levels they had from all different versions.
Also, story for me is a very important factor. Regrettably, here it is almost nonexistant, and what is there, is worthy of a fanfic...a really bad one. It doesn´t explain convencingly why Umbrella was gone, why Leon became an agent, there is no motivation to any of the enemies Leon has to face. Sure I´ll admit most of MGS3´s bosses are as cartoony as they come, but at least the main bosses had a clear motivation and a fleshed out backstory. RE4´s had none.
Controls, as well, need some work. RE4 really did needed a strafe function or at least some way of sidestepping, hugging walls is not ideal in the least. Also, moving while shooting is very important, and RE4 still neglected it.