Currently population imbalance is the biggest issue for me. When you log in and see Vanu at 24%, TR at 32 and NC sitting at 44% and all you get as VS is a 1% increase in XP you just laugh and most likely go to another server as you will just get farmed.
For one they need to increase the bonus for underdog factions and maybe even need to cap faction population in some way.
What might play into this is that even with an organized team it is way to hard to impossible to hold a base against an unorganized zerg. Often it's wiser to just leave and cap something else. There is too little incentive to actually defend bases and also it's too hard to hold against a zerg.
Currently it feels more like to zergs rushing at each other and outfits flying around in Galaxies "backhacking" stuff and ignoring the larger fights. Especially on underdog factions as there is no use in fighting if you know you cannot win.
Also I think they should increase respawn timers on Galaxies and give the Sun a mobile spawn certification. But that's not really balance related