Here's the thing about control mechanics in MGS2, they seem difficult and clumsy because everyone has become accustomed to the CoD layout from the current gen FPS/TPS.
This is borne out by the fact that nobody had any issues at all using/adapting to the MGS2 control set when the game released, in fact they were a joy to use. However, going back to the HD conversion years later and they just can't adapt. I find it difficult and I'm not even a FPS/TPS player in general.
I do think the MGS2 layout was a deliberate choice to force the player to be deliberate and slow in their action, after all it's a stealth game before a shooter. Aside from boss fights, nearly the entire game can be completed without firing a single shot.
During the PS1/PS2 era, developers were very splintered in their approach to control layout, whereas everyone currently aims for uniformity (because of the "if it don't control like Cod, no one will play it" attitude
).