There is no end game, or middle game tbh, infact the entire game is just click flashy things and kill space ships, beam down and kill anything that moves, rinse and repeat. Come back in 2 years and end game may have arrived.
In STO endgame is asking where's endagme content while waiting for episodic content. Then getting those episodes and completing them in 20 minutes or less only to find yourself asking "where is endgame content?".
My point is, as long as we keep getting these missions that don't take long to complete, but do monopolize development time, we're not going to see any.
Expand exploration to be explorable and fun. There are several really good threads on how to do this. And also, open PvP in some form or another. Start putting the resources in more sandbox elements.
Last time I checked there were over 100 missions on the Foundry, and it will probably be closer to 175-200 by the time it goes live. The Fed side currently has around 50-55 Episodes in it - the rest of the missions being patrols and exploration. Assuming 20 minutes each mission 180 missions is about 60 hours of additional /played time. That will hopefully keep the power-gamers like myself busy for a couple of extra weeks.