UPDATES 12/06/10
Bubble Crab
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It’s looking great! Is sigma going to be the final boss? and if so are you going to have a final form of sigma?
That would be ideal, but I'm not sure yet. I'm definitely going to have Sigma's primary forms from each game though. They're pretty ideal for a fighting game anyways!
If each Sigma is going to be its own character, then you could have each final form as a super. As for a final sigma form? If you can do a 16-bit form of Sigma's final form from Xtreme 2, that could work (I mean, you did put Berkana, so Sigma shouldnt be a problem)
Nobody in this game is going to have any supermoves whatsoever, actually. I should have mentioned that before..
I was considering his Xtreme 2 form though. I'll probably figure out the final boss situation once I've made a considerably large roster.
Awesome project you have here. I really like the filtered sprites for the project.
I made some MMX styled Axl sprites a month or two ago, you can use them if you want and edit them however you want. I pretty much went off from the one Axl fake screenshot for Megaman X9.
(Some required poses may be missing.)

i demand a template for making custom MMX chaacters such as this!!
http://www.sprites-inc.co.uk/files/X/I don't know if this is what you mean, but this website has plenty of sprite sheets!