The two big omissions (from my perspective) were Telenet and Masaya. To drill down more specifically, I think Valis III would be the best choice because it’s emblematic of the system and was localized. And on the Masaya side I’d want to see Shockman or Shubibinman 3. The former was localized and has cute Mega Man vibes and the latter is pure 90s anime ridiculousness.
From a personal perspective, I simply adore Monster Lair and still play it regularly, which I’ve been doing off and on for 30 years. As one of the earliest CD games and one of the two launch CD games for the US, I feel it has a good claim to being there. Plus, clearly Sega played ball with Space Harrier.
To digress a little (segeuing from Space Harrier) it was interesting to me to see from the selections and conversation around the MD and PCE minis, which games mattered to Japanese players that don’t matter to the western audience as well. China Warrior was clearly hugely (pun intended) important to showing off the system’s power in Japan in 1987 but I don’t know anyone in the west who cares about that game at all.
Also say what you will about it, but how can it be the TurboGrafx mini without Keith Courage? Seriously.
I wish I could point toward a western-developed game for the system that I’d want to see on the mini but I’m coming up dry. Loom?