I loved the Delta Flyer! You could take the in game runabout, add in a few more weapon slots, add hull strength, make it fly almost like an escort, but still, it would be a small craft. Also be sure to upgrade the boff stations.
Now the most important thing, is to give the Flyer a reason to exist. Release shuttle missions, where the plot has you launch a shuttle from your ship, then you control the shuttle. A normal shuttlecraft comes free, or you can buy the runabout, or at endgame levels buy the Flyer, and use the small craft to go through the mission.
The captains yacht could be a part of all this too.
