Definitely Dark Cloud, whether it's a reboot, spiritual successor, or a sequel, I'd be welcome to that.
Weird how no one mentioned Star Fox; the recent title was just a remake of the Nintendo 64 game. Shigeru Miyamoto said something about the game not being popular in Japan, maybe in other regions as well. It might have to do with the Adventures, Assault, and Command changing what the series was about so much; action-adventure game, improved/expanded on-rails space game, and something that went more like 64 than Assault. It was rumored and suggested several times that it that a Wii Star Fox game would exist, but nothing happened. Hideki Kamiya said he'd like to take a spin on Star Fox for the Wii. And some other developers were considered for a Star Fox game for the Wii U.
Same goes for F-Zero, I don't like racing games, but I'd love it if Captain Falcon was more than just an iconic Super Smash Bros. character.
Jak & Daxter really deserves a comeback after what happened with The Lost Frontier. And considering that Playstation All Stars: Battle Royale features several Sony first-party characters, they could use that to their advantage to bring Jak & Daxter back like how Konami/Platinum Games and Capcom/Ninja Theory did with MGR: Revengeance Raiden and DmC Dante.
Soul Reaver and Legacy of Kain. I love the voice acting and story of the game, even though I never played it. For a PS2 era game, it had a wonderful script compared to current games.
Shinobi? The game with the life-sucking katana and badass named Hotsuma. No other reason, but to have another badass ninja to compete with Ryu Hayabusa. Just retcon the series Sega, just do it.