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.
This already is the case with commodity traders. You can buy certain items for less from various brokers at different outposts. There are even deals found on Vulcan and Andoria. Prior to F2P, different stations offered different equipment for the various marks and medals but when things changed over to dilithium the need to fly to a particular base went away.
I would agree that to stimulate traffic at most outposts there needs to be more reason to go there especially since it no longer takes very long to level up. People don't spend time near SB39, or battle group omega, and soon no one will need to go to Bajor or DS9. In the beginning, it would take you quite some time to get to VA but with F2P that was changed to speed people to end game content. I think BORG mod items should be put back for purchase at battle group omega and put romulan items at SB39 or new romulus. A RP type game shouldn't be buying from your UI tray for everything. As it is now you won't need to to fly anywhere, just open your PVE queue and join a queue and when you level up on your UI system just buy right from the screen. It sounds more like zynga and farmville on facebook than an MMORPG.
I think the players need to choose to not use EC to warp directly to missions. In other words, just because its there does not mean you have to do it. Otherwise, this board would be filled with threads asking Cryptic to give players the means to warp to their missions.
Regardless, I actually agree with the OP on this issue. All starbases don't have to be the same.
And yet how much stuff in this game is already spread out specifically to function as a time sink? Go to DS9 and how many laps do you run because the STF kiosk is on the opposite side of the station from the bank terminals? Or the DOFF grinder being on the opposite side of SFA from the Exchange broker? No logical purpose, other than to consume time. Why add more?
I agree, so long as each SB is given an equal role. Like honestly, I would've preferred having the Omega Force stuff originally be on K-7 and Ganalda respectively. DS9 became a major pain to deal with since pretty much season 5 began and they changed the STFs, slow loading for most, so season 7 will at least alleviate the pain of that.
But yeah, special stuff for each station, which you can only find there, would help ease the burden of more major stations, such as ESD and DS9.