A scan of a flyer available at E3 is currently running around the Internet, and it clearly shows the game being in 3D. The strange thing is that almost all elements of the screenshots are from X1, so the possibility of this game being a remake exists. Note that Zero's back for another round (don't ask, I don't even know myself...) You can see the scan directly from the article at MMO.

News credit: Megaman Outpost