With the success of BSG among sci fi fans, may i suggest that the next star trek series present a more darker theme to its story telling. These are the following ideas for 1, 2 or 3 episodes story arcs.
1) A starfleet captain is bought to trial after discovering that he had ordered ,rather relutantly , the torture of captured Cardassian officers, in order to gather infomation about enemy bases and fleet movements during the Dominion war. The starfleet captain did this in order to minimalize starfleet casualties.
(a storyline that corresponds to contempory usage of waterboarding by the USA under george w bush)
2) A human scientist who performs lobotomy on aliens that he captures and kepts them as servants as he is prejudiced against non humans.
(yes, racisim still exist in the 24th century)
3) A starfleet ground combat unit that carrys out an unintended massacre of a ferengi colony near the ferengi/federation space. the ferengi are all killed down to the family memebers including women & children. Starfleet starts investigations & brings those involved to trial.
(similar to the my lai massacre incident during the vietnam war)
4) A entire race who are members of the federation starts to suffer a horrrbile genetic disease that proves incurable and causes their extinction. I nominate the denobulans as the soon to be extinct race as we see them in 22nd century (Enterprise Series) but not in the 23rd or 24th centuries which could mean that they are slowly dying off.
(In the babylon 5 series, there was this race called Markab who eventually die out due to a disease)
5) starfleet tolerating and even working with slave owning cultures along its border and federation citizens owning slaves and homes on those planets outside federation control.
(interesting moral issue, brings up the issue of states rights versus slavery which was a big issue that caused the american civil war)
6) Starfleet encounters a race where there are actually three genders but but the third gender is often killed as soon as they are born as they don't seem to have any use. That race like most races require only two genders to procreate but in their distant past, they needed 3 genders in order to procreate but they evolved from that to now only needing 2 genders. Because of that they kill the third gender because they have no use for that gender anymore.
(Gender rights issue)
7) A gay klingon, i want to see how how klingons deal with the issue of homosexuality. Who knows, may be they are more tolerant than we early 21st century humans are.
8) zombies in space. We could have an episode where a starfleet medical ship picks up hundreds of sickly patients from a colony who slowly die and then reanimate as walking zombies. The starfleet ship becomes infested and the survivors fight back. We could have a "the walking dead" type of situation onboard the ship as the survivors await for rescue.
(zombies. I love zombies ! The TV series Andromeda had an episode about zombies infesting a ship but i always felt Star Trek could do it better.)