Tatsujin mentioned that Chiki Chiki for PCE plays badly on the PCE compared to the MD version, but, I think it plays just the same as the MD version. I have both, & they feel the same too me, it's not like comparing the choppiness of the PCE Strider to the smoothness of the MD version.
As for Raiden, the SNES version looks like crap compared to the SNES version, & I mean that! I figured that everone here would have the same opinion, when looking at those pics. The gfx on the SNES one of extremely plain & boring to me, not just the lack of vibrant colors, but, the lack of details that the PCE version kept. The only things going on for the SNES are the 2 player co-op(which is nice) & the paralax(which is minimal IIRC).
Valis 1, the Genny version, for the most part, is alot plainer looking. There are parts where things are done differently, can't quite say what looks cooler in some of the areas, however, ofcoarse the MD one has paralax, which after Valis 4, you would've thought that Valis 1 would've had as well.