Some of the PC-98 games sold like 200 copies. There really wasn't a fan base until around PCB. PC98 not so much.
For the first part of the topic, I would enjoy seeing a game for a handheld system, but between the [3]DS[i ]'s split screen and the PS3's small screen, it would be quite hard to put a shooter on them. Maybe a game with a throwback to HRtP style gameplay, or a fighter, or some other spin off would work, but the genre doesn't lend itself to a small screen well.
I would personally love to see some PoDD characters (<3 you Ellen and Kana), Elly, and the MS cast return, but I can see how some of them would be hard to explain their absence. And I could not figure out how to word that last sentence. As for Mima, I personally like the character's design and PoDD theme, but it would be awfully hard to explain her disappearance without hanging a bittersweet lampshade on it.