I'm going to cheat and nominate whatever I feel requires a sequel. Why? Because you can't stop me, that's why.
Chrono Sequel. Okay, sure, the connection between Cross and Trigger is tenuous at best, but it's still a great game. Hell, even if you try to put the two together I think Cross comes out on top. Yeah, I said it. Do you like your sacred cow medium or well done?
But I digress. We need another game (Chrono Break or Chrono Crash were always fan favorite titles) to continue the Chrono legacy of greatness. More music, more instantly likeable characters (fewer than Cross though, everyone agrees 42 characters is overkill) and darkhorse characters (just bring back Magus, and we're golden) and more twisty-turny WTF plot-twists.
Just one change: Have one of the Western developers do it. Maybe Bioware, if their hands aren't full. Chrono Sequel could even benefit from a slightly more action-adventure vibe, something like FF12/13.
Super Maro RPG: *insert subtitle pertaining to plot*
Paper Mario and the Mario&Luigi games are lots of fun, and I love them all. I admit nostalgia might be playing a role in this opinion, but Super Mario RPG: Legend of the Seven Stars was and still is a benchmark in what makes a superb RPG, and in the time of lack-luster JRPGs, we need a title that is recognizable, yet isn't on its way to being an out-right joke (i.e., Final Fantasy).
Just one thing I want to include: Talking. Just make Mario soft-spoken, who shows his emotions with actions... and his mustache. How awesome would it be if we almost never saw Mario's mouth because it's covered by his mustache, and that's what does half his emoting?
As for who should make it, well, I think Square-Enix could do well with this one, just as long as they approach it with the same respect they did with Kingdom Hearts. They made FF+Disney work, I think they can make FF+Mario work a second time.
Final Fantasy VI-2. I believe it was someone on these very forums who suggested a Mega Man 9/10 style reboot for the Final Fantasy franchise, and I agree wholeheartedly. Polish the pixels, maybe cheat with the music a little, and the rest falls into place, I think. Malignant soul of Kefka's residual god-like powers, evil/insane Espers, a new oppressive government super-power, any of these plot devices work to set the story in motion.
Square-Enix could make this one too, no problem.
Warcraft IV. If Starcraft 2 can be made, I don't see why we can't have more Warcraft. Besides, how unbelievably awesome would it be to draw on the lore created in Wrath and Cataclysm for another Warcraft RTS, only for Blizzard to turn around in the future and expand on it in WoW? The mind boggles. Well, mine does, at least.
Furthermore, outside of the hero characters, WC3 wasn't too terribly unconventional. There have been leaps and bounds in what we might consider mainstream and desirable in an RTS game since WC3, some of which, sadly, aren't even included SC2 (hero characters come to mind, barring maybe two or three certain levels). WC4 is just what Blizzard needs to innovate the RTS genre beyond anything we've seen so far, and in the process, give their Warcraft universe a much needed injection of fresh lore and story.
Mega Man X9. Like MM9&10, MMX9 with super-polished sprites, or maybe even something akin to art animations. More awesome metal/pop/whatever genre the MMX music falls into. And it's Mega Man X, there's no need for a story! We can throw one in, but it isn't too necessary. You vs. a bunch of Mavericks modeled after some animals or plants or whatever. There's a beauty to the series' simplistic formula
Castlevania DS. I loved every single DS incarnation of Castlevania, even if they were all the same game with different characters and (some) bosses, but dammit, it just works, and we need more! With more new game+ features and hidden stuff and bonuses, because I'll be honest, the DS games have been lacking in replayability a little.