Well, awhile back, I'd had some interesting innovations that could be implemented into a Megaman game. Granted it would take eons to code in GM (maybe), but I can't say it wouldn't be cool to have in the series.
SKILLMIXER SYSTEM
In this, of course, Megaman would still get special weapons from the bosses, but not only that, he would be able to mix and match different weapons to get new ones. For example:
Atomic Fire + Air Shooter = Burning Syphon (Or something like that, you get the general idea.)
The combination of weapons would be used to solve complex puzzles on maps, or to create new utilities that Megaman could use to help himself along.
COMBO RUSH SYSTEM
Instead of having Megaman just shoot his buster, he could chain attacks together like so:
Punch+Punch+Kick+Kick+Finisher(Flipkick)
OR
Kick+Kick+Flipkick+Slidekick (Would send enemy into the air...)+Finisher(Chargeshot)
Stuff like that. Also, a juggle feature'd probably be cool too... but probably wouldn't work so hot on bosses.
That's all I could think of as far as the classic series goes, would have been cool if they did something like this for *cough* MegaMan 9 instead of regurgitating the old stuff again...
If anyone wants to do something with this, kudos to you. xD