Huh? X2 was essentially the same as X1, except with some gameplay refinements. It's still a great game, of course.
Well, so.. It's like this.
Picture Megaman X as one big-ass tutorial
game meant to set up the story for the players to understand the situation and environment, the circumstances that the characters live with. If you look at it like that it kinda makes sense.
Every fight kinda leads you or points you toward the end goal of beating Sigma and the game, but the entire game is pretty much spent teaching you basic shit (basic for a Megaman X pro, anyway), even the weapons are simplistic in their function and natures.
Then Megaman X 2 comes, with an array of much more complicated and dangerous situations you're thrown in; in Megaman X you could come into a room and notice a spike or pit trap, and the game gives you adequate time and ability to consider how to deal with these obstacles.
But Megaman X2 isn't like that at all; instead you are more often thrown headfirst into a dangerous situation with no way of knowing the terrain or impending dangers other than having traversed the level already. But if it's your first time, how would you know if there's a huge pit of fire, or spikes at the end of a long fall you're supposed to jump down?
If Megaman X is boot camp, Megaman X 2 is actual
war.
I hate to break it for you, but Capcom never cared about the story.
They cared enough to cheese it up for fans in the hopes of profits. After X3 I think they realized fans were more concerned with blowing stuff up, to consider caring to make the story make sense; they wanted to change too much, and it convoluted the story into something that would embarrass Kingdom Hearts fans.