For me the PC Engine version is so watered down without the shop, which by far and away makes the Genesis version much more fun to play.
With the Genesis version allowing you to pick the order of your stages, as well as plan out how to save up money to get the best equipment (or focus on other things like magic or health), it makes it far more versatile - this more than makes up for some extra colors on the CD port. It was hard to quantify but playing the PCE port in Ootake it just felt looser, control-wise, than the Genesis port. Sega really did a great job reprogramming Capcom games on the Genesis, and Chiki Chiki is no exception.
Honestly, if you're not going to get the Genesis port, I would not even bother spending the money on the inferior Super CD version. Burn it on a CD-r and then come back to us to complain about the game's awful sound effects.