It would seem that the Shuttle Pod was unintentionally made a purchasable, deployable and usable ship in 0.6a and Alex sees it as a 'Bug' to be fixed.. as mentioned here:
http://fractalsoftworks.com/forum/index.php?topic=6980.msg114338;topicseen#msg114338I personally like it, sometimes use it as a means of travelling between systems relatively unhindered at a low fuel cost, or ferrying mothballed ships.
The game mechanic could also be such that when your final fleet ship is destroyed this is the one you're stranded in and you have to make your way back to civilization to buy another ship or fleet.
You could also have the shuttlepod like a personal command vessel that gives an additional +1 to your Command Points.
Anyway, Alex, don't delete it regardless of other cool new suggested mechanics! It shouldn't be difficult to 'un-fix' the ship into existence.
