Peace Walker controls fine since it's MGS4 controls. MGS3 is 75% fine since it's Subsistence version with real camera but there's still some "press triangle to climb" instead of just pushing against a climbable object.
MGS2 still controls like MGS1 and plays like the PS1 game.
Not that I think there's anything wrong with those controls. When I replayed the entire series (including Portable Ops) a few years back they all held up and controlled great. Never had to think twice about anything, but then I grew up with the series.
Only thing that really makes me sad about this collection is the MGS3 nightmare sequence was cut. That was one of the best "WTF OUT OF NOWHERE" moments, break the 4th wall moments, innovative moments, in gaming history even if the mini-game was shallow and repetitive. Apparently it ran on a totally different engine so it was too much work to get it in

The other missing things like small effects here and there don't bother me and the pros of this collection are VERY great (60fps MGS3, dual analog Peace Walker, 5.1 audio, online play in PW, clean widescreen MGS2/3, etc...)