I'm still fairly new, but do have a Fed char up to rank 38, and have been wondering for some time now if I need to buy a small craft in game. Do these have their own missions or are they purely just for fun. Because their defense and fighting stats suck compared to regular vessels, so I just dont wee the point in having one unless you must have one to play certain missions.
There are a few missions and a couple queue events that use them and don't allow a full sized ship. The first time you get to one of those missions, you'll get a free type 8 shuttle, but I'd strongly advise you at least spend the energy credits on a runabout, since the type 8 has no boff slots at all.
They have their own missions; two each for Federation and Klingon, three for Romulan (Not counting the KDF mission where you steal a Federation Runabout).
"The Vault" (Cloaked Intentions FE series), "Operation Gamma" (2800 FE series) and the Romulan 'Attack on Planet Hoth' mission where you in your small craft lead a bunch of civilian fighters to defend a city against Elachi walkers.
Or, as I personally like to call them, the "Give Turbo a ruddy headache and make him wish he could just call in his REAL ship to blast something - seriously, who says to themselves 'I want to pilot a shuttle'? Nobody! If you wanted to fly a fighter, you'd buy a flight simulator. Why play STO? Because you said to yourself 'I want to command a starship'" missions. Yeah, they make me rant a little. Explain to me, for example, how a Kivra Toron Shuttle is somehow more stealthy than B'Rel Bird-of-Prey with a cloaking device just because they're smaller...
As a Fed you get a free Type 8 Shuttle for your mission, but I went ahead and bought a Runabout.
Also, if you want a spoiler, read below. If not stop here.
I loaded the free Hargh'peng torp on my runabout and beat a Mogai. Since then I always store the free hargh on my small craft. The explosion radius also catches groups of fighters, and if the target is alive for the secondary explosion this also takes out fighters.