Dark Cloud 3 - Level 5 probably won't return to their root's, since their later franchises are much more financially successful.
A Final Fantasy that is like the first 9: explorable world map, turn based battles (without sudo-MMO aesthetics
Aquaria 2 - the team behind this neat indie game dissolved years before I even discovered it.
Someone beat me to the rest:
A true continuation of classic Sonic- Sonic 4 doesn't feel like Sonic 4. Sega probably never will make a game that feels like what would come immediately after Sonic 3 & Knuckles.
Spyro and/or Crash - Activision seems to be done with both, the former because he did his job to make Skylanders into its own hit franchise and the later because no one can come up with good concepts anymore.
Klonoa - If he ever comes back, it will will probably be a small game on mobile or 3DS eshop, since these games have a kid-friendly look and sadly never sell well enough.
Jak 4 or a reboot that goes back more to the original's gameplay and mood - There's no signs of Naughty Dog returning to Jak, despite the first game alone having enough world building alone to make more amazing adventures.
Games already mentioned above that I think will be made:
Mega Man Legends 3 - If Red Ash (or maybe just Might No. 9 by itself) proves to be a success itself, there's no way Capcom is going to let the knock off run away with all of the money. The execs likely just need proof of the demand for MML3. They're probably also looking at the sales of the PSone classics, too.
A good Metroid - Metroid's always been one of Nintendo's lower profile franchises (like Star Fox, F-Zero, Kid Icarus, and others) that seem to get dusted off for a few games, then shelved for years. I have no doubt they'll make another well received entry. The real question is will I be registering my unborn child for school by the time it comes out? (Have I even met her/his mother yet, too?)
