Late response is late, but: this is incorrect. =p IV had the full 108 list, although the number of playable characters in that list was noticeably smaller than in previous titles. You might be thinking of Tactics, concerning the list, as it pretty much ditched it entirely and just gave you a bunch of characters to recruit.
As for my own response, let's see... Well, any form of re-release whatsoever of the Suikoden titles would be a godsend, and Konami's a bunch of idiots for not milking that potential cash cow, but don't get me started on that rant... Parasite Eve would be an amazing choice for a complete HD re-haul from the ground up, but if we're just talking about a remaster, then something from the PS2 era would probably be preferable, so hmm......
Well, I've been wishing for an HD collection of the first three Fatal Frame games for a while. That'd be awesome, although I've pretty much given up hope on that ever happening. (Plus, they're all PS2 Classics now, so at least there's that. Also, makes them kinda "not count" for this thread, according to the original post.)
So aside from the Suikoden games, I guess I'd like to see some Front Mission games touched up. Especially if it meant getting a local release of FM5, since that one never made it out of Japan. I suppose there wouldn't be much of a purpose in upgrading the graphics for that type of game, but judging by FM4, at least, Square never implemented the component cable upscale feature, so it would just be nice to be able to play FM4/FM5 on an HDTV without it looking like trash. Doubt it would be worth doing anything more than a PS2 Classic release for, but I enjoyed FM3 (PSX) and FM4 (PS2) thoroughly, so I think it'd be nice to see the series get some love.
Looking over my PS2 collection, I'm not really seeing many others I'd like to see updated, though. Maybe I just never expanded my horizons enough back then. ^^;