I can see that this idea may be unpopular with some, but here goes.
I think that all starbases should be given exclusive functions that necessitate the need to travel to different sectors. Quite simply, there should be no "one stop shops" in the galaxy.
Currently (before season 7) ESD, DS9 and Memory Alpha contain EVERYTHING that a player needs, being bank, exchange, officer training, shipyards, respecs, borg equipment, crafting and fleet construction. This renders some starbases, suck as K7 and Starbase 39, superfluous.
I think each base needs to be able to have a forte, something that it can either do exclusively or at least better than anywhere else. Perhaps have a trader at K7 who can provide replicated gear (antigens and the like) cheaper than anywhere else. (Handy for those feeding starbases, embassies and reputation.) New Romulus should be the only place you can get Romulan gear, even though it's through reputation. Earth should be the only place you can train BOFFs. Make DS9 the Borg reputation shop. Basically make the MMO a little more realistic in regards to space.
I can see people already formulating their arguments against this idea. Still, I provide this idea to promote a touch more realism (yes, I know it's a game, but realism in the right place is a wonderful thing), and it will encourage well designed game elements to get more usage, other than the 5 seconds you're there for the story. Maybe spring surprise missions on people as they're travelling to certain starbases, like a cargo ship under attack, a random encounter, etc. Just like the TV series.