BOTF is certainly un-matched. There is no other trek game that compares i think.
Indeed, I would have to agree with you. Of course Armada 1 & 2 are both strategy titles, but they lack the Civ-style empire-building aspect of BOTF.
Given the dearth of Civilization games out there, I'm shocked that BOTF hasn't gotten a sequel by now. I know there's a fan made version coming, but imagine the money that could've been made...
*sigh* Your sentiments echo those of many BOTF players over the last decade. It's always been somewhat puzzling to us that neither (now-defunct) Microprose nor any other game developer ever saw fit to create a sequel.
I suppose they shot themselves in the foot by releasing the game too early and not adequately beta-testing it first (there's no denying that vanilla Birth of the Federation is an *extremely* buggy game). After that, everything else would have been the proverbial "fruit of the poisoned tree"; since the game's sales and reviews were both rather mediocre, any developer would've felt like it wouldn't be worth their while to create BOTF 2....