2 months since last post, but it's not like much gets posted around here anyways...
I think Zero plays a huge part of the problem surrounding X's character development, but he himself is not the problem. Personally, I think the biggest problem is either:
A) the result of different interpretations of X's character (I can't prove this)
B) the lack of a developed personality X is supposed to progress towards in the first place
At first in X1, Zero is what X is supposed to become. Then in X2, he comes back, so obviously they're going to have to distinguish between two characters with defining differences. However, this contradicts the point of the first game: to become like Zero. The solution? Have X gain SOME Zero-like qualities post-X1, but not all of them. For starters, X has always been about pacifism, while Zero is about business. X pre-X1 is naive and way too idealistic, so if not in after X1, then at least throughout the series, X becomes more realistic with fighting Mavericks, but not to the point he forgets his ideals (or maybe even lose them only to regain them again).
The SNES games did this right because, back in the days, it was mostly "show, don't tell". Seeing how they had little dialogue and centered on a guy who singlehandedly took out armies of Mavericks and their badass commander Sigma, you'd think the guy have some spine and a little hardened personality, right? In X2, X starts off the story as THE 17th commander (originally Sigma): he's starting to become badass, and even the X-Hunters know not to underestimate the person who fell Sigma in X1. In X3, Doppler too does not underestimate X based on the last 2 games. Basically, even in the little dialogue that was given, X was portrayed as someone to be reckoned with, so naturally he had a cool factor, even with Zero right next to him.
Sadly, with technological advancements, when they weren't spending all their cutscene budget/story time on Zero, the devs decided they wanted to flesh out X's naivety because they couldn't the last 3 games. Unfortunately, it's now already the fourth+ installment. You could say that, after X1, X wasn't even developing as a character anymore: he just became a static, idealistic nice guy that contrasted with badass, straight-to-business Zero. Anything X accomplished was pretty much forgotten and everyone just treated him as "some hunter". You'd think after stopping 3+ wars, people would give the guy some respect? On top of that, X4~X6 decided to focus on Zero's origin story, while X7~X8 were dedicated to Axl's origin story. So in other words, after the SNES trilogy, X got completely shafted in terms of plot development.
Mega Man wasn't ever really much about storyline, but I always believed a game could still have a good story and memorable characters through show, don't tell. If Samus could do it, why not X? Instead, the writers decided to simply stick to what's already established rather than possibly changing X for the better.
If I could change things, what would I do? For starters, give X more badass time post-X3, the guy looks like a pussy until the Zero series when he's "dead". It's fine if he's naive here and there, but at least SHOW that X eventually becomes more realistic and experienced as a war veteran. It shouldn't take X7 for him to figure it out that maybe talking can't fix everything and that innocent civilians are dying while he sits at base doing nothing. Thankfully, X8 didn't suffer this nonsense.
With Zero returning in X2, ideally the series would focus on their development as partners: what one lacks, they gradually gain by learning from the other. X learns to be realistic from Zero, but Zero learns to understand that there's more to just slicing up the bad guys. And if introducing Axl is such a necessity, at least introduce him during a point where X is also a respectable badass who eats Sigmas for breakfast.