Man... if I even knew where to start with something like this, I would be all over making an enhanced version of Chorus of Mysteries, with updated graphics and music.
Well, I can help with the hardware interfacing of the PCE. You can limit yourself to just write 6502 code, and interface with the hardware directly too. I've been thinking, I could create some library functions to help interface with the higher colors/sounds/CD tracks/ADPCM/larger cart size, etc.
I hate to sound stupid, but what's the point in this besides "Oh, I can do this!"
It's neat and all, but are you planning on doing something with it after you port them, or what?
Actually, that's was original part of the reason for doing it. Not that "I can do this", but more of "hey look, play some NES games on your PCE (real hardware)" for the PCE community.
The second aspect was for hacking. Which is why I posted about it here.
If you didn't know; the PC-Engine has up to 481 colors onscreen without any tricks, has 4bit tiles and sprites, has 16x16 to 32x64 sprite sizes(in increments of 16x16 cells), up to 16 cells or 256pixels of sprite data on a single scanline, has 64k of vram, has built in support for scanline effects (doesn't need a mapper or external interrupts), can write to vram at ANY time including active display (no 8/16bit console system allows this), has 6 audio channels in that any of them can play wavesamples or each channel has a 32byte buffer for custom waveforms, has fine stereo control over each channel, has two hardware volume control levels for each channel (which are logarithmic. most useful than linear volume steps), has master pan/volume for all channels, and can be up to 8megabits without a mapper and 20megabits with a mapper. Of course, that doesn't include the benefits when they are made into CD projects; play any CD audio tracks, stream data like FMV or custom style cinemas, full 64k of ram for an ADPCM chip to play really rich samples, etc. And if you use a CD project, you have all 6 original channels free to do whatever. There's also the fact that the CPU, besides having more addressing modes and instructions, is 4 times faster @ 7.16mhz. If you need more processing time.
So those are the possibilities for upgrades.

So far, except a few situations, sprite flicker is reduced and slow down is removed. But none of the projects I posted has any other upgrades done to them. They still have the same audio limitations because I'm emulating video/audio hardware (and there's missing audio emulation still). It would be up to a hacker to assign FX to the additional channels. I do have a CD project of Castlevania that hacks into the music play routine and plays CD audio instead, but that isn't public yet.