Ideal for a sequel...
>20 or so weapons, with at least one being a melee weapon, no more mr.zurkon or disco ball (it's been done to death)
>Racing, Quark mini games or something similar
>Arena with platforming challenges as well
>Multiple planets with more than one mission, less linear, more paths
>Jetpack over the fast boots from CiT, or if so, both
>Multiple planets
>Comfy hub similar to the ship in UYA
>Go back to the tongue n' cheek and somewhat inappropriate writing the original games had
Also, remember the crystal mission from GC and the sewer crystal mission from UYA? Bring one of those back. Make it rewarding with massive bolt gains, and bring back the interesting new gadgets or items too!