I've been playing with Exerelin and several of the supported faction mods for a while now. My current campaign is 24 systems, 5 stations/system. I think 9 factions total.
My character is up to level 42 now and one thing I am noticing that bugs me, is that a faction will send 30-50 fleets to capture an enemy station, while leaving 1-2 fleets to defend a station they own. To make it even worse, factions will gang up on a station with their allies.
When I get the notice that one of my stations is being boarded, that station is gone by the time I arrive and they are on to the next one. When I get into the invaded system, there is literally 100+ fleets there, and maybe 4-8 of them are my faction. This is no exaggeration.
I find the only thing that can possibly stop a station from getting capped is if I have a fleet strong enough that no enemy fleet will attack me, and I abuse the hell out of the 'Repair in Station' function. I camp the station, blowing up enemy fleets as fast as I possibly can, while keeping an eye out for the dozens of Boarding Fleets that are incoming. Eventually they give up and move on to some other target (probably one of my Allies stations).
With the current faction fleet behavior, there is no hope in hell that a faction can defend a station without my intervention.
I will say that yesterday while protecting a Junk Pirate (My Allies) station from invasion, there were about 15 enemy fleets on my screen and as I had the game paused, mousing over them looking for Boarding Fleets, I noticed that every single fleet on the screen said 'Hostile, running from your fleet'. It made me feel pretty badass.