Honestly, if you wanted to make a 3D Mega Man X game, do the company and your fans a favor and make an Action RPG out of Command Mission.
It'll alleviate the platforming frustrations since your team is mainly focused on developing a closed-bottom RPG world and introduce movement strategies including location and terrain to boss battles, and the fans will appreciate the lack of random battles and the re-addition of the combat mobility that makes X and co. so powerful (i.e. avoiding attacks and accessing the Charge Shot a heck of a lot sooner). There would also be the ever-important replay value if there were 2 difficulty modes OR a New Game + where you can play through the whole game as a different character (wouldn't even have to change the story, provided they're present at the beginning). One playthrough of the RPG, you might be X. Next time, Zero. The next, Axl. Fits right in with MMX:CM1's ending.
Now you might be thinking, "Wait, wait, wait, Super Paper Mario and Sonic Chronicles underperformed, and you're suggesting this?" Yes, because for every bad Action RPG there is out there, there are as many good ones (Tales of ____, Kingdom Hearts, etc). The idea is to keep the game simple (and I would DEFINITELY recommend a KH1-esque Lock-On), but give it the addictive brevity of a platformer.