The "Cross Genre" thing is a weak argument. Again, see Super Mario RPG with Sage.
Also, most of the characters being ranked are INITIALLY from MMXCM. Worst case scenario, we're ranking the 6 PCs, which means half of those are MMXCM originals (Massimo, Marino and Cinnamon), and frankly, I wouldn't be shocked if a lot of people were introduced to Axl through MMXCM (I know a lot of people have never played MMX7 or MMX8, but have played MMXCM in the DL, for example), so really, its just X and Zero who have this "issue" that isn't really much of one.
Considering the game will be ranked as "Mega Man X Command Mission" and not "Mega Man X Series", there won't be any problems. Much like how, again, Mario, Bowser and Toadstool/Peach are ranked as "Super Mario RPG" and not "Super Mario Series."
If the Sonic RPG were to suddenly get enough support (doesn't seem likely in the near future...sadly...), would you use that same argument against them? Really, its not a significant enough point.
Heck, Mario and Bowser get around this DESPITE having potential vote splits based on M&L and PM series; Vote Split is a MUCH bigger problem, if you ask me, than "Cross Genre." Cross Genre should not be a factor; if the game is a reasonable to interpret RPG (which MMXCM is; Sonic RPG is too for that matter, but that's not on trial, only mentioning it since I brought it up earlier), then it has every right to go up for ranking.
At least in the case of, say, Kingdom Hearts, you can say the game has issues that make it potentially unrankable; the fact that some don't consider it an RPG is the big one, but other factors like "No Damage Display" (you have to eyeball everything through Scan) kick in and the game becomes something people like to avoid. But a game like MMXCM that is an RPG through and through, with no real issues based on the game itself? There's no excuse to hold off on it.
Being weary about the Vote Draw is one thing; that's fine, its a reasonable argument. But "Cross Genre" is silly, especially when it really only matters for 2 characters, and KIND OF matters for a 3rd, and there are cross genre characters in the DL already and they've never had this problem.
Heck, many people were introduced to Ike through Brawl, and to them, Ike's a Fighting Game Character, and not an SRPG Character, do we hold this against him? Of course not.
To take things a step further, to almost everyone who isn't a fan of the series, Marth is from the Smash Brothers series, *NOT* from Fire Emblem; the "he originates from Fire Emblem" is like a minor point that no one cares about stateside since no one played the game he's from. So, FEDS is coming out soon, should that game come up for ranking, are you going to hold that against Marth cause most people view him as a Smash character and not an FE Character?
SMRPG has advantages over MMXCM, I won't deny this, but as far as the Cross Genre thing, they're the same. SMRPG's big edge is, of course, more people have played it, but that's why its ranked and MMXCM is only now up for it. But really, very few people, if any at all, are going to take this "Cross Genre" aspect into account. At most, its going to be write up material (and its good stuff too!), and not much beyond that.