First of all, get rid of the X-buster charge mechanic. In the actual Megaman games it's annoying to use, makes an annoying noise, and just creates problems in other aspects of the game design. If you absolutely must have a charge weapon, at least make it auto-charge whenever you're not shooting, like in the Game Boy MMX games. I hate having to hold down one button 90% of the time while trying to do jumps and stuff (not to mention the fact that if you're doing this for PC, most keyboards can only recognise about three keypresses at once).
With that gripe out of the way, the most important thing is probably just to always keep in mind the issues that Megaman games have by their very nature. They're kind of like RPGs in the sense that their difficulty curves are basically backwards. The game starts off difficult and then gets progressively easier and easier, until there's a huge difficulty spike once you hit the Wily/Sigma Stages. They've tried different ways of getting around it; MM3 had the Doc Robot stages, MMX6 had the bosses get more powerful over time, etc.
One other peeve of mine is that the system of weapon energy and extra lives is set up in such a way that it's often better to kill yourself and continue from a game over, rather than struggle through a stage with a disadvantage. I personally think that's terrible design. This was probably the main reason X5 had that weird time limit system, and the Zero games do weird things with continue penalties as well; just to stop you from dropping yourself down a pit when you run out of Rush Jet.
It'd be real cool to have the various weapons have more utility within the stages themselves, rather than just being there to exploit a boss's weakness. Stuff like throwing blocks around with Gutsman's power, or grabbing items with Boomer Kuwanger's boomerang. In a perfect world, each weapon would interact with many stage elements in cool and intuitive ways.
Also, with X they started doing neat things with stage order having consequences. Like Flame Mammoth's stage getting frozen after you beat Chill Penguin, or flooding Sting Chameleon's jungle by defeating Launch Octopus. I'd like to see more of that sort of thing.