I'm working on an edit with that same intention. I posted about an earlier version
here. I've kept the Ferrengi edits -- I think it's really cool for their ships to actually be worth capturing. But I've backed away from some of the other edits and kept them mostly stock. In the latest version, I've given the T'Khasi Orion a TWarp drive and turned the CargoTran into the Super CargoTran: 200 holds, 4tpw, and TWarp... and made it available only to blues.
There are a lot of other ships that still fall by the wayside. Nobody in their right mind would ever fly a BattleShip or a StarMaster, for instance. I haven't thought much about other ways to make ships interesting. Since offensive and defensive odds are separate stats, it might be interesting to make some ships offensively weak but defensively powerful, or vice versa.