I'm going to say a major problem with X5 and X6 was that they started you out with armor. If an MHX 5 or 6 were made I'd actually like to see them do away with bringing back the armor from the previous game.
I would agree with this. Starting with Fourth Armor in X5 was ridiculous. Designing stages around Falcon in X6 was stupid (Unarmored X has a better charge shot, so he actually has a tradeoff). Giving air dash to Unarmored X and Shadow would solve a lot of the immediate design mistakes, though I'm not so sure what other repercussions that might have.
I'll touch on X6 just because I'm sure it'll be a hot-button issue: I'd leave the core level design EXACTLY as it is. However, ...
I can understand the reasoning to be an absolute purist, but some of the stuff from X6 is inexcusable and would need some tweaking. Flame already mentioned Heatnix and Sheldon's main path.
That roly poly spike segment in Yammark's stage is inexcusable. If people [parasitic bomb] on MM9 for trial-and-error stage design like Splash Woman, there's no defense for this part. You should never force a situation where a player is <i>punished</i> for having to guess.
Scaravich's stage being random is simply dumb. You shouldn't have to visit the stage multiple times on a search quest while being a victim to RNG. This amplifies the stupidity of armor sets because you have an armor completely reliant on the player stumbling on one of its essential pieces. They should've let you choose a path, e.g. touching either the upper or lower half of the totem poles determines your path.
Wolfang with Heatnix's nightmare effect is silly. How they expect you to dodge everything is unreasonable.
If you're preserving the oddities of Gate Lab, the essential parts like Hyper Dash and Jumper really need to either be moved around or at least hinted on their importance. Not okay to underplay what is considered mandatory by neglecting to mention them. Or when they do mention them, they really, really [tornado fang] it up:
Alia: A High Jump Part will be help.
One more thing I would add is the known facts of what is possible postrelease, i.e. "unintended" things. For example, I firmly believe Capcom intended Shadow to be obtained using Blade, and thus, <i>after</i> Blade. It's a commonly known fact that you can get Shadow Body in Turtloid's stage by simply tanking a hit and dashing through the spikes. The problem is, removing the exploit rubs purists the wrong way, but leaving it in comes off as extremely tacky in terms of design. If your intention is to allow players to search for either armor in whichever order, the requirements to completing one of them shouldn't rely on obscure and nonsensical methods. Forcing a hit on the player to advance is <i>not</i> okay, as witty as it might sound.
The obvious solution would be to widen the gap to not necessitate a pixel-perfect air dash, but then you would be taking away what is considered a "feature" of Blade.
Also, The [tornado fang] was with this bit in the boss rush stage..?
Was this supposed to be a misleading path? Why would anyone fall for it? The one without the spikes will obviously be more appealing.
When I was young, I honestly thought that path was a secret that led to an armor capsule or something. I think expecting reason out of Capcom's design choices is asking too much.