The main advantage of the super grafx that would have been the most noticeable, were the dual background screens, this would have been great for large bosses, as for the double the on-screen sprites, i just played 1941 yesterday and noticed quite a bit of flicker, there were allot of sprites on the same line of course but i have seen more impressive stuff on cd. I am sure the extra system and video memory would have been great.
When comparing to normal hucards, you have to remember that 3 out of the 5 Super Grafx games were 8 Megs, the vast majority of pc engine games were 2, 3 and 4 Megs, in fact, i find Magical Chase (a 4 Meg game), especially the 1st level in the US version, to be graphically more impressive than any of the super grafx games from a artistic and color stand point, but the game also has good parallax, animation and shadow effects.
As for cd games, yes, many of them far surpassed what was on the super grafx, compare Winds of Thunder to Aldynes, Rondo and Beyond Shadowgate to GnG and Grandzort or Sapphire to 1941.