PC Engine has noticeably more vibrant color than the Genesis. I detected that even when I was 6 years old. Lots of Genesis games are pretty washed out and ditherific. One of the prettiest Genesis games to me is still Phantasy Star II. I like it more than 3 and 4. 3 is dithered to the max, (but still my favorite PS game)
Other than that, the PCE is at a disadvantage, really. One background layer makes doing some things a bit painful.
If you sit nicely done PSG tunes next to the Genesis, depending on preference, it's at an advantage there. The stereo effect in games like Dungeon Explorer should be easily noticed by even the doofiest of people.