I just started playing and while looking through the ships available I saw the option to "purchase" shuttles, runabouts and fighters.
Now I am trying to figure out just when and where choosing to run with such a ship would be preferable over a Lt. cruiser or larger vessel. I undestand that the smaller ships are more maneuverable but can they really handle ship based missions in the game?
Basically, the sole real purpose for playable shuttlecraft is that they're required for three missions (Vault, Operation Gamma, and the Vault Event). Although they're all much more maneuverable than any other vehicle available to Starfleet (the slower shuttles are comparable to Birds of Prey, though), even a Miranda is so much better that there is no real competition.
On the other hand, in the shuttle missions, I wouldn't recommend using the free Type-8... a Danube Runabout is fairly cheap and offers much better performance, even if you don't spring for one of the C-Store shuttles.