I think the more accurate term would be reboot, but yeah even Starfox 64 as awesome as it was was a reboot of the original SNES Starfox which I don't think gets enough recognition. Your point is still valid though, they reboot the Starfox franchise way way too much which makes it suffer from things seeming a tad repetitive. The Lylat System is where the Starfox team lives, but I think it would be well served if they did a bit of world building and branched out to other solar systems of whatever galaxy they are in. New planets have been introduced over time, but most of them have been old planets with some changes, albeit some that make them seem completely different in some cases.
The World Ends With You: This is a highly underrated gem for the Nintendo DS that has one of the best sound tracks of any game on that system. The story revolves around shinigami which are the Japanese equivalent of grim reapers and is an interesting mix of Japanese mythology and the modern real world. There have been some hints of a possible sequel, but nothing has been said about it for a long time which is a shame.
Banjo Tooie: I know there was Nuts and Bolts, but it just wasn't the same. We are thankfully getting Yooka Laylee as a spiritual successor, but another Banjo and Kazooie game in the style of the old N64 games would still be awesome.
Conquers Bad Fur Day: This will unfortunately probably never happen, but it almost did. This raunchy over the top game can still make me laugh just as much as it did when I was younger.
Star Wars Knights of the Old Republic: The Old Republic MMO is quite good (though the sidequests can get a tad repetitive if you play through multiple different stories), but I would still love to see a Knights of the Old Republic III.
Actraiser: It had a sequel which was decent but not as good as the original. The best way to describe Actraiser is it is an interesting mix of action platforming and literal world building. The main character of Act Raiser is a god who must gain worshippers to gain power, he does this by slaying monsters and building cities for said worshippers to live in. With the dramatically expanded AI options available now as well as other advancements if done right a sequel could be truly amazing.
Prince of Persia: This series has been around a long time but really got awesome with the Gamecube trilogy that began with The Sands of Time but after it dipped in quality rather significantly. The sands of time mechanic dosen't need to be done again as there are plenty of other things that can be done, but I would like something a bit better than some of the more recent entries.