Now I understand why its different. MW2 give you no reason why they are killing the civilians. They just do it because they hate them. GTA doesn't have much of a reason other than the fact that hes an angry out of control immigrant, who is being attacked by the Siberian Mafia.
The reason for GTA's is a lot sillier sounding, that combined with the amazingly fail physics makes it an adult cartoon basically.
In MW2, they head in for a completely serious reason, and are more realistic than GTA, thus making the entire setting more serious and more wrenching to the viewer/player.
Honestly I think that the creators of MW2 achieved their purpose of 'make people hate terrorists' quite well really, because some (note the word SOME) people watch that and think "what the forget is wrong with these people?" and come to the conclusion that they are heartless, spineless people who want nothing more than to bring terror into the hearts of everyone so they can gain control/whatever the hell they want.
As for the other games mentioned in comparison to MW2, I don't know because I haven't played those; but as far as comparison between GTA and MW2 goes: MW2 is far more serious.
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