I think it would be really cool to do an infulltration mission. You would get surgicaly altered to become klingon, cardasian etc and youi have to sabatage something i.e a ship, outpost colony.
You could going around planets killing certain klingon who are at threat to the federation.
This isn't Splinter Cell lol however infiltration missions would be pretty good. There have definitely been times in ST where this has been done. The only thing I don't agree with is killing an enemy through infiltration. There is already too much killing in this game and it has taken away from the feeling of being in Starfleet. If there was an infiltration missions it should be to rescue someone, imo.
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Check the Intelligence Missions link in my signature.
Like go to a klingon colony under cover i.e surgicaly altered. And have to give or find some top secret data etc.