I would have loved for an updated Karnov (the NES version) for PCE. That would have been awesome. Of course, I'd want a Super CD version, with the equivalent of 2 long quests (the original quest, plus a new one), and the option to have PSG or Red Book Audio soundtrack.
Then we have Gyruss (Konami). I'd love a really souped-up version, with special flourishes and effects (and, if it didn't break gameplay, a variety of creative backdrops). Always the PSG/Red Book option, which you can switch on the fly, and some "dodging" sequences.
Then of course, my ultimate dream, is an updated version of Mega Zone (Konami), with a special "horror mode", made just for me, that is so intense (in terms of sound effects and soundscape), that it scares the hell out of me (and you).