Here's how I invision the Starfox DS game should work:
At the beginning of each mission, you're given a map of the level and use your stylus to draw a path through it. There will be branches, but you're not allowed to backtrack, so you must choose wisely. Although maybe there could be a power-up that lets you change your path mid-level.
Then you enter the mission, flying along the "rail" you've drawn. The controls are the same as the original Starfox, except with the extra tricks added in Starfox64. The stylus won't come into play at all, except maybe with bosses, because they always need some sort of gimmick.
And that's it. Sweet and simple. Don't fix what ain't broke, Nintendo.