Ideally, I too would like to see Runabouts to be usable in conjunction with your main starship.
To launch them and switch between them would be particularly useful in collecting anomalies.
In combat, they would have to be automated like however Klingon fighters work from their Super Carrier though.
I would also like to see other ships like this end up in game.
This game has the potential to allow one to select from dozens of classes of starships with differing abilities and roles. If it can pull that off, it might just make it as a top-notch space MMO. If it relegates all of our end-game fighting to 2-3 ships, the boredom will set in pretty early.
watmo i point you to voyager and the delta flyer which in essence has the same functionality and size as a runabout,
I personally don't like the idea of using them like fighters because that's just not what federation ships seem to be about but being able to deploy one for anomalies and what not would be very nice as well as just fun.