as much as i personally like metal gear, there are just some nuances about it that bother me slightly.
1.) the cyborg ninja type character (gray fox, olga, raiden), with all its fancy moves, being able to slice up bullets as they come, manhandle metal gear rex, destroy gekko like they were dolls, just can't seem to lay a finger on snake, who doesn't really show any of those 'wow' moves and simply relies on weapons. i dunno, snake beating gray fox in single combat without weapons just doesn't make sense to me.
2.) snake/raiden fighting bosses and yet afterwards still maintains his stealth. obviously not an issue in mgs4, but in the previous installments he fights bosses, kills them, then continues to sneak around the base as if nothing happened. since he fought the bosses, obviously his presence has been detected and i would think that the guards would be more alert. unlike regular alerts, which can all be avoided if the player is skilled enough, boss alerts can't be avoided so its just an odd thing that the rest of the base doesn't care about these events.
3.) the codec, which according to campbell in mgs1, can only be heard by snake. but when he speaks, shouldn't he be heard by the guards surrounding him?
4.) stealth camoflage was used by otacon in mgs1 and he seemed to be able to move freely everywhere. according to him, there were 5 stealth prototypes in his office, so why didn't he just give snake one then and there? on the whole, if stealth camo could be manufactured as such, why doesn't snake just use them in all of his missions?
5.) when snake is caught in predetermined encounters (wolf catching him and ocelot torturing him, then the 4 stealth guys in the elevator in mgs1, the frogs surrounding him in act 5 in screaming mantis' room in mgs4), why didn't they just kill him while he was in those compromising situations instead of letting him live and eventually escape, even when they tried so hard to kill him before and after?
6.) otacon losing a loved one in every metal gear seems to show kojima hating on his kind of person. in mgs1 he lost sniper wolf, in mgs2 he lost emma, in mgs4 he lost naomi. is kojima just picking on him or what?
7.) if one man can destroy metal gears so easily (think raiden against 3 metal gear rays at a time), what's the point of manufacturing them in the first place?
8.) in mgs3, snake can easily change camoflage in the menu in stopped time. how does it make sense that he changes clothes right in the midst of a hostile environment while at the same time never having his camo index to go low?
9.) how do rations and other food items heal bullet wounds? this is why mgs3 is the best game of the series for me, because it was able to run away from the food = life mechanic. in mgs3, you had to put splints on broken bones, apply antiseptic on infected wounds, ointment on burns, and you would continue to bleed and walk gingerly if you don't heal yourself. i'm surprised kojima went away from this in mgs4
10.) octocamo is able to mimmick the background, hence making snake practically invisible at times. good. but what about the gun he always carries around? the guns dont have any octocamo capabilities, so why doesn't carrying and/or firiing a gun not lower his camo index? even if they can't see snake, what's preventing them from seeing the gun?
11.) where does snake put all those huge things that he carries around (drum can, multiple missile launchers etc.) that he can just pull it out of nowhere? I rather prefer Uncharted's way of dealing with it, only allowing two weapons to be held at a time. far more realistic than pulling a rail gun out of nowhere when its convenient.
don't get me wrong, i love mgs. just wanted to see what you guys thought about these little nuances :D
(EDITED for accuracy)
and Wii 
