"Clearly" is a dangerous word to use, but here goes:
Just didn't want to hear minor stupid details like "in japanese version, bonk has a gray pixel here whereas in the us version it was corrected." Nice input btw. All news to me.
Bonk's middle forms are feminine in the PC Engine versions. I prefer the North American forms, because it's a natural progressions which also better fits the overall theme.
I think that Zonk's bomb is cooler than giant turds, but Denjin has the cool intro. More people seem to prefer Denjin, but I like how the music syncs up in Zonk during the intro.
Godzilla is better on PCE, because the quiz mini-game lets you earn enough points to unlock every form.
Dragon Slayer is clearly better on PCE, because of the CD2 extras.
I think that the original Booby Kids theme works better in Cratermaze than the Doraemon version, but both have great music.
I don't like the Adventure Island intro, so Dragon's Curse is better.
Exile WP is broken, so Exile/EXR II is better.
Exile seems to have not had any cuts and the fading in/out static is fixed, so it's better on Turbo-CD.
Gate of Thunder's three bonus games make it clearly better than the PCE version.