Black Tiger, I know we're on a PC Engine forum and everything... but c'mon. A little intellectual honesty, here?
http://tg-16.com/screenshot_comparisons_action.htm#Valis_3
As illustrated in those shots, the Genesis has the better detailed backgrounds, more layers of scrolling, and a less dim color palette. The issue of cut content does not factor into this equation. Advantage goes to Genesis.
Music is a toss-up. Some tracks are better on the Genny, some the PCE. If I was forced to choose, I'd probably give the edge to the Genesis, just because it has this.
Regarding the cut content... normally this would be a problem, but since the aqueduct section was part of what got trimmed, I'd argue this is a positive.
Curiously, you didn't bring up the controls in any of your rebuttals, and it's easy to see why. The PCE version is clunky and less responsive in comparison, there's no denying this. Genesis has a dedicated button for sliding, less delay on projectiles, magic comes out quicker, certain magic attacks are more effective, smoother jumping, you can turn around while in crouched position without standing up (later levels in the PCE version can be quite frustrating due to the lack of this ability)... as important as aesthetics are, gameplay is king, and even if the PCE
did have the superior aesthetics, I'd still pick the Genny over it for that reason alone.
Again, I'm not knocking the PCE game, it's one of the more enjoyable Valis titles, to be sure. Just that it's outclassed by its Genesis counterpart, is all.