There's a huge potential for a good exploration system if they based it on Star Control II. They should look at the way you could talk to the alien races in that game and build alliances with them. And combine that with a colony building system like Eve Online and a resource gathering like Mass Effect 2 and 3 (which was also based on SCII). Mix it up a little with the DOFF system and we have something feeling more like Star Trek here.
Go speak with a NPC and give him one of three possible answers that lead to either succes or failure? That would get old REAL fast. (Actually you can find that in the game, Tau Dewa sector, Accamar system).
People often want vague things like "more diplomacy" without an idea on HOW to do that. It's pretty much impossible to have a meaningful, diverse and repeatable computer generated diplomacy system. The only thing you would get are a few pre-written dialog trees you can climb through over and over.
I've posted this before, but to say it again: I'd dearly love the mechanic from The 2800 where one of the ambassadors gives you Doff missions INSIDE the main mission that contribute to your success (if you complete all three you get a dialog option to sway him to your side). I thought that was brilliant, and the technology for it already exists inside the game.
Also, there was the one-off mission in orbit of Bajor where a Cardassian Gul is being accused of treason and you have to investigate the evidence against him. Brilliant mission with very creative use of branching dialog and unlocking new dialog options and glowie item actions.
And we have the mechanics from STFs with optional award bonuses if you achieve specific conditions. We have seen optional in-mission goals as well on a few occasions but none of them outside the STFs are linked to rewards.
We have the class-specific mission goals. In Colliseum, Tac officers build a fire, Engineers cook food, and Science find water.
In Frozen we see a mechanic where a dialog choice determines which of two factions treat you as an enemy in the resulting battle.
In the Defera breen patrol daily you have the option of peacefully escaping or starting a fight.
Bring all of these mechanics together and use them more widely. Give many more missions optional goals with increased rewards attached to completing them. Give many more missions uncertain enemy factions or where battle is optional like in the breen patrol. Let us use our Doffs during missions to get an advantage or complete a task.
This is all technology that already exists. Just use it more often.
Actually, one of the reasons I loved New Romulus is because I really felt like I was exploring - both because the territory was so darn big, and because a lot of the missions (and I did them all) are not combat.