Well, from a start, IMO, I don't see what place does take Syphon Filter with MGS. There's no comparisson in between. Just that you use guns in them (don't get me wrong, I LOVE Syphon Filter, but I just don't see the similarities.....
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Syphon Filter controls were awsome, that is, for that kind of game, which I find best in its genre.
Now, Metal Gear Solid has it's own genre if you come to think about it... it's not just an action game, is more like a RPG as well... kinda hard to describe
And I actually think that MGS' controls could not be better. They just fit the game perfectly IMO.
As for the FPS online thing...... it'll be alright to me as long as it is just a feature and not a wholeness to the game. In that case it would suck.