Metroid: since 2002, Nintendo has left us with a cliff hanger right after reviving it from an 8 year hiatus. They only released interquels that while being damn good (except Other M) did nothing to address the fact that Samus just became an outlaw in the eyes of at least a few high ranking Galactic Federation brass. And Ninty had the gall to announce Metroid Dread and then cancel it while ignoring 6 years of fans pleading for a new 2D Metroid. Sakamoto supposedly did not like the Prime games very much(thanks in part to Japan's dislike of FPSs, maybe), but they are loved over were Metroid actually has a stronger market. Plus they need to drop all the story telling they've been trying to do. Prime's scan logs and Fusion's monologues were enough to flesh out the story without breaking the sense of isolation that makes Metroid great and atmospheric. Even the Prime series slowly got guilty of this by 3 and Other M script should have been thrown out the second Samus met up with another team.
Either they need to make Dread, expand on the outlaw plot they basically sent up at the end of Fusion, or give Retro or another good American Developer free reign on another 3D Metroid.
Jak and Daxter: I loved the first game. It had a extremely interesting, magical world to build upon. The eco puzzles and abilities were great and could have gotten better with sequels. The series could have gotten even deeper with the Zelda style exploration. Instead they had to fused GTA into it. Gone are the colored eco powers, the great for all ages story, and the magical land to explore; here's some scifi guns, an anti-hero, and another post-apocalyptic wasteland for you. While I did like Jak 2&3 and they did still have some of the magic of the first game, they just felt like they don't belong with The Precursor Legacy. Naughty Dog needs to dust this series if they still own the rights and either retcon it right at the end of the first game(unlikely, but look at the Highlander Films it can be done and make at least one good sequel) or bring back the magic of the first game( no gta style missions, blue red yellow eco powers/puzzles, less emphasis on guns and Dark/Light Jak). Though a sequel regardless of direction would be nice.
Final Fantasy: Pretty much everything above posters have said. If Square must make the main character a bishonen, make him likeable sorta like Zidane, not an asshat like every male lead since. And, bring back the explorable world map of 1-9. Realistic graphics is not and excuse that it wouldn't work. Even with a decade of 3D models the party still stands in place or makes no effort to avoid the massive easily telegraphed attacks, and that's still accepted by fans. We still got the feeling of immersion whether our character was towering over most cities on the map or when they stood emotionless while the giant magitech demon charged up his mana beam. Square is too obsessed with eye candy to make a decent game since 12 was in production. Not to hate on the other composers but the soundtracks have been mostly bland since Uematsu's departure, and Sakaguchi's might have been the signal that Final Fantasy 10 really was the final one. Maybe they should look at their past for inspiration and make another FF9 style throwback to get the team's creative juices flowing again for the next game after that.