I like the idea of auxillary craft.
1) Shuttles come and go; sometimes you have extra, sometimes you're short. It's hard keeping track of which shuttle goes where and belonds to who, so let's avoid the hassle by making them freely exchanged between ships. The aux. craft would be there to stay, though, and could be customized (mainly thinking as in interior setup here).
2) Plot wise, it's good for giving the characters another place to hang out and another way to get to where we want them to go (for example I'm sure some couple will use it was a secret dating/make-out spot).
3) Shuttlebays could be eliminated entirely through the use of docking points.