I'll admit I like Zero better than X. I mean, he near always has a kickass theme music, and in his first appearance, he blows the arm off the intro stage boss. That said, I happen to like X too (the absence of Model X being a major letdown for me with ZXA), and I especially like seeing X and Zero as a team. Didn't appreciate X4 taking them each solo.
As far as X6 goes... I just don't like the fact that you have to use parts if you go unarmoured. I would have liked to be able to finish the whole game without touching a part or armour, much like pretty much every other X game. Oh well.
Well, at least you're specific enough that it's actually true (I keep catching people claiming that it's one given part/armor which is necessary, which is not true), and you put it into context with required upgrades not being completely alien to Mega Man games. That being said, X6 is the only game besides X5 in which you can proceed with no special weapons. And X5's method of doing so is rather cheap, having you just flick an option in the menu screen to screw over the world.
I like X6's head-scratching stage obstacles because it's never a matter of "only one thing works", which is what Mega Man level design typically amounts to. X6 runs a bit deeper than that by presenting obstacles that have multiple solutions. Oddly enough, despite his previous reputation as the "advanced" player, Zero is often the easy way out of such situations.
X1 is my very close second favourite, hindered only by the fact that you have no choice but to get some upgrades (barring passwords, of course)
I don't believe any password will get you past Zero's death and thus prevent you from picking up the buster upgrade. FYI, MHX allows you to skip the leg upgrade without the need for hacking. Although I personally have a hard time getting used to any post-3 MegaMan game with no movement faster than your basic walk (my main gripe with Rock in 9/10).
Also on DeviantArt, Rumble, DLive.tv, and the Fediverse (@freespeechextremist.com and @bae.st)