In the game epilogues, X has pretty much always questioned whether or not violence was the answer, ever since X1, but throughout the main body of the SNES games he has too little dialogue for it to show (X3's manual also references this, IIRC). X4 was the first time this properly showed in game dialogue, and coincidentally a character of his type takes fighting former allies hard (ie, Dragoon and Double), plus the whole voice acting thing, made it all appear a little more heavy than it was probably meant to.
It's hard to justify X7 as anything but giving people a reason they have to play as Axl. In gameplay I don't mind so much because X is powerful enough to justify his late entry, but in storyline it makes very little sense. X is halfway ready to throw Axl to the sharks at the beginning of the game, and he is not supposed to be THAT naive.
Command Mission represents what X's typical character should probably be: He believes in what he is doing but some part of him can't help but wonder why the enemy would instigate the level of violence that they have. A person's motivation seems to be where X focuses his attention when it comes to judging character. While it's not particularly difficult to win his trust, he doesn't easily forgive betrayal, and he recognizes a simple lust for power when he sees it.
X6 is perhaps X at his strongest. One of the few times the battle was personal for him, X shows almost no sign of hesitation, no matter what the enemy's reasons or how great their power. Rarely do we see him that determined, yet he still holds onto his compassion in the end.
In addition to his big heart, I think it's also because X is so old that his enemies tend to underestimate him, but around Xtreme2's timeframe the more competent villains began to realize what a mistake that was. Since then, a villain's take on X tends to be a good indicator of how simple-minded the villain is. If they're just full of themselves, they won't take the little softie too seriously, but an intelligent opponent knows that X is a force to be reckoned with, and a constantly growing one, at that.