I have always had the idea of ending the original series with the X series. In X9, you could kill two birds with one stone.
Duo, or perhaps another character from the original series could come back into the X series. Upon his return, he mentions certain events that accured during the past, with that said, X and Zero set of on an adventure to dig up some unknown ruins. Of course there would be bosses, but instead of having elemental creatures for bosses, Warrior Alienoids could be the new set of bosses. Such as Shinobi Scorpnipod or Pharaoh Griphinx and Yamato Komodrako.
In general, they find out several things about there past, such as what happened to Mega Man and the rest of the crew? What happened after the Zero onslaught in the original series?
Honestly, I believe the game would make insane sales, and Capcom could regain some of the fandome who got lost and outrage during the lose of plotholes.
It'll be a smart move.