What do you mean they don't use fighers in the ST universe? what do you think a shuttle craft is?
DS9 we saw them a lot in the battles with the dominion near the end, espeically in the big one where they came back to take DS9 back.
Also in the Stat Fleet Command game, you had many types of shuttles (or fighters
The idea that none of the races in the ST mod being different makes it boring is wrong, if you want different atmospheres, just don't use the mod, the mod is setup to be like ST ... plain and simple.