For Jak 4, I'd personally enjoy an expanded Wasteland and Haven City. Perhaps more things to do in Spargus and the Naughty Ottsel. Various little oddjobs that give you skull gems or orbs?
Me, I'd like to explore the areas around Haven City more. Perhaps a return to Snowy Mountains, or even better, maybe the ruins of Gol and Maia's Citadel?
1. Setting (this might require time travel)
2. Eco in its pure form (they can keep the Morph Gun as well, and Light and Dark Jak)
3. Characters (bring back Gol and Maia, perhaps expand upon the Red, Blue, and Yellow sages)
4. A classic Jak look (make him shave!)
5. Scout Flies and/or Power Cells... maybe (they would have a different effect than in the first game, though, most likely)