Where do you even BEGIN to list the PCE/TG16's missed opportunities??? There are so many! As was mentioned previously in this thread, the SuperGrafx in and of itself a was a HUGE missed opportunity. Maybe not in Japan. That thing was going to fail there, no matter what. But if they'd have delayed the US release a few months and released the SGX here in the US with, say, 50+ quality PCE games, the western market (for the most part) wouldn't have even known any better that it was derived from inferior hardware. Then you'd have a situation where the PCE was still getting plenty of support in Japan and the SGX would have been getting support in the west, similar to the Genesis (assuming NEC America would have marketed the thing properly, which is an awfully big assumption).
As for software, the list is basically endless... the PCE never got a Contra game (seriously, Konami?). A proper conversion of the original Teenage Mutant Ninja Turtles arcade game would have filled the beat-em-up gap quite nicely. As would a conversion of the Battle Toads arcade game (it even used one of the PCE's native res modes, 512x224). Final Fight as a 8 or 12Mbit HuCard would have been pretty faithful, I'd imagine. Mortal Kombat was originally planned as a PCE *exclusive* but NEC's higher-ups turned it down because they thought the fighting game genre was losing steam (just... lol). A proper conversion by Irem of R-Type II would have been nice, and completely doable on the PCE. Black Tiger would also have been dead simple on the PCE using the SAME engine Capcom used for Son Son II (seriously, go play them both back-to-back... they're essentially the same game). And, yea, the platformer library on the PCE was seriously lacking. Also, not that I'm a huge sports game fan or anything, but some greater support by EA would have done wonders for the western market. They finally threw TTI a bone in '93 when they made Madden Duo Football or whatever it was (it was essentially a CD-ROM version of Madden '93), but by then it was too little, too late.
Then there are the quality Jp region games that never made it to the states. That list is quite long as well. Rondo of Blood, Gradius I/II, Salamander, Spriggan, Kaze Kiri, SFII' CE. It goes on and on...