What are small crafts (shuttles, fighters, etc..) good for?
 

Except "The Vault" and the DeltaFlyer Daily?

Or are they just in because they're seen in the movies & shows?

So far there aren't any other missions in which use of small craft is mandatory, but they can also be used for just about anything where you don't have to fight enemies that are too powerful for a shuttle to face. In good hands, the fighters or Delta Flyer are about as strong as the Tier 1 ship.

Which is the grand majority of the content in the game..lol

Join shuttle wars on the weekends - small craft pvp and deep space encounters! :D

Mostly for fluff. Like all the uniforms, basicaly, but with more mechanical complexity behind it to make it work.

And shuttle_wars:
Shuttle Wars PVE Edition: http://forums.startrekonline.com/sho...d.php?t=226433
Shuttle Wars 2.0 (PvP): http://forums.startrekonline.com/sho...d.php?t=224500

Not only for missions where you don´t have to fight, with the right equipement, strategy and teamed with other guys in shuttlecrafts, you can take even on the most powerfull enemies. Its longer, you die more often, but its also much more of a challenge..
Our fleet just finished the Cure in shuttlecrafts this Sunday. 4 delta flyers, one runabout, so they can be used for nearly anything.. =)

Target practice?

But seriously, there are other parts of the game where shuttle/runabout use is inferred... like boarding parties, or new bridge officer assignments, etc.

And let us not forget the shuttle-type pets.

Shuttle use is also depicted in other missions. You use one to pick up the Vulcan ambassador for the P'Jem mission. I believe there is also a KDF mission where you steal a shuttle to penetrate a Federation facility (haven't played it yet, but I'm looking forward to it).

Really, it's just added Star Trek flavor for the game, and that's a good thing. I'm sure we'll see more shuttle missions in the future now that the shuttle tech has been added.

they work fine at tier 1, and i suspect more shuttle based missions will be coming but yeah they are kind of a novelty, for private pvp, or roleplaying.