I enjoy Starsector more due to a few factors for me.
Factor A - The Ships/Combat - I'm specifically talking about the ones that allow you to phase skim / teleport / activate maneuvering or plasma jets. Anything that allows great to insane levels of mobility is a huge plus for me. Warlords does this as well with the Sublight Drive, allowing even cloakers to get into position and do high burst damage, but it just doesn't feel the same when the enemy is able to take your shotys and dish them out twice as painful (I use Plasma Cannons with Shockwaves on a frigate currently, the plasma cannons do not feel like plasma)
Factor B - Descriptions - A detailed description of the ships and their purposes is always good, and this is one of the things Starsector does better than Warlords, like for example, buying a new frigate and knowing how fast it is from standard (unless al ships are the same with just hull making a difference) or weapon locations even. Being able to tell where the weapons are located is one of the most essential factors for combat/salvage.
Factor C - Style - This is more due to absolute personal preference, due to playing Starsector for so long, but I think 2D Top down really seems to do it for me, less complications, seems faster as well. Although Warlords does feel a bit more exhilirating as a result of 3D, I do like seeing all of the details painstakingly handmade/handdrawn.
Factor D - Weapons - This one is simple really. Starsector has more "true" ballistic weapons, weapon sizes, diversity, feel and overall likeness to the weapons. Currently for Warlords, there's Beams, Railguns and Plasma Cannons for light weapons. Heavy Weapons are also restricted category wise, to just three/four (?) weapons.
I can see myself constantly playing Starsector to fill the void in my soul that Starfighter once took alongside Alien Galaxion X.
Starpoint Gemini : Warlords, however, eh not so much.
(QUICK EDIT) - I have only played Warlords since yesterday, so this is probably why. (Oh and your fleets will die very quickly)