If the destiny only stops at planets with gates, theres no use for the shuttle, just use the gate to get there of course. (unless you could use it to explore planets quicker, which would of made sense for air part 3)
But then the destiny won't stop anywhere else, where the shuttle could be useful.
So pray tell, what could you use the shuttle for, other than a plot device? Also didn't it have a broken window in air part 1? whatever happened to that?