So, here's how I'd fix the X series. Boy, there's a lot to discuss with that one, isn't there?
First off, we'll start things off by returning to the original 5-game premise that Inafune had wanted in the beginning.
Add more story factor, like in MHX. Revamp the beginning game by using MHX as a base. We'll also incorporate Xtreme 1 and 2 into the first three games, perhaps as a canon-friendly bonus for beating X2 and X3. In other words, we'll continue the story: they are bonuses, but it is canon. Also, with Xtreme 2, you have a chance to develop Zero and Iris's relationship, so you can make Iris a better character and help improve the fourth game.
Naturally, X2 and X3 would be a bit different as Dr. Cain apparently gets nuked in MHX (don't argue with me, people, the standard anime formula more or less shows him getting nuked. I'm not debating it.) But, the general theme for X2 and X3 remains (Rebuilding Zero, and Doppler and Sigma's collaboration). However, include more references and influences from Wily in these three games.
X4 would have to be done much differently, but the general plot will still be used. First of all, give General and Colonel a much more solid, much more believable reason for starting a coup. Then, remove Magma Dragoon, Cyber Peacock, and Split Mushroom from the mainstream boss battles. Make them endgame bosses like Colonel, Iris, and General instead. Why didn't I mention Double, you ask? That's easy: Double's inclusion was pointless. His role could have been done much better by, you guessed it, Magma Dragoon. By replacing Double with Dragoon, you can increase the tension factor when Dragoon is revealed as a traitor. Also, Dragoon makes a much better double agent than that bumbling metallic tub of lard ever could.
This goes without saying that fighting Dragoon should be a much more difficult, but that much more awesome, boss battle. Again, include his reasoning for betrayal (wanting to fight X and Sigma giving him the chance). Meanwhile, continue on with the basic tension between Zero and Colonel during the Maverick uprising. This will naturally put a strain on the relationship between Zero and Iris, which will eventually culminate in the battle where Zero is forced to defeat and destroy Iris, causing heartbreak and angst for the Bishie-Bot.
Again, have Wily influences in X4. Goes without saying.
Finally, we reach the X-series endgame: Mega Man X5. Again, we'll stick with the Eurasia plot. However, make Wily's influence in this game much more obvious. Also, make the colony drop feel that much more urgent. Go back to the anime cutscenes. Make it so that the game gets harder as Eurasia gets closer. In the end, have Wily himself appear as a boss alongside Sigma.
And of course, make the final boss X or Zero, depending on the character you choose. And make the battle epic. I mean absolutely epic. Make the character much more difficult (X was irritating with the Ultimate Armor and X4 attacks, and Zero was just lame in the current X5) and give Zero a much more solid reason for turning on X and the Hunters. Tension across the games (especially with Iris) can influence this, such as more connections between Zero and the Maverick Virus.
Naturally, the ending of the game would involve X's victory over Zero, and X taking the Z-Saber in memory of his friend. Leave the ending open for MMZ1, and then proceed to revamp that series (but leave Zero 1 alone, that game was pretty much perfect).
If you do the multiple endings for X5, make it so that they all tie into one another, not have radically different ending scenarios. This gives replay value, as to fully understand the end of the game, you have to take all the different routes to see each side of the story.