What would be nice for a new Star Trek game would be a single player roleplaying game. Build your cadet, do various duties (ship and ground), get promoted, ... until you are your own captain. At this point, get assigned your first ship, then get to slightly customize your second ship, and nearly fully customize your third ship. (Example: Picard's movement from the Stargazer, to Enterprise D, to Enterprise E.)
At that point, you can make the choice of continuing to play this "era," or be promoted to Ambassador (back to mostly ground missions) or Admiral (Command and Conquer tactical missions.)
The inspiration for the above: Spore's delineated era system.
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As for my personal ranking of the television series, from high to low:
DS9 (Overall story arc instead of being episodic.)
TNG (Grew up watching it.)
VOY (Overall story arc and got to watch it.)
ENT (The show sunk because of its constant scheduling changes on UPN, thus I wasn't able to watch it.)
TOS (I don't like Kirk as a captain. Spook's integration into TNG was wonderful, though.)
In the end, I hope the reboot of the genre makes its way to the television. (I could easily see a Babylon 5 style series.)