STO seems like a very granular experience. Like things have been created and placed within the world for just one purpose, one mission, one objective, cut off from the rest of the galaxy by both form and function. A star system isn't really a star system at all, its just a small area with a couple ships and rocks and a single planet in it and its totally unrelated and unconcerned with anything thats near it. Its very...well...granular.
What if the locations were integrated instead? What if entire star systems were simulated and within this simulated star system you had solid and perceptible connections with what happened there. You deal with the Crimto or the Starlians so that you can chart the anomalies in the system without being harassed. You chart the anomalies so you can understand how to stop the earthquakes and volcanoes from destroying the native warp capable species. You then give them aid and they clue you in to where the Borg are staging their attacks from. Finally, the entire thing comes together and you eliminate the Borg threat from the star system all together; at least until tomorrow.
This change would go a long way to 'filling out' the STO universe. Im not saying Cryptic simulate every cubic kilometer of ever star system in the whole galaxy, but at least the planets and maybe moons of the important places. It would also work well with a change in scale between us and the cosmic objects we come across. Imagine being awe stuck by the Jovian moons with Jupiter itself in the background. Wow.