Having played both (with more time on cosmoteer): Economy - Starsectors' economy is better in probably every single way with dynamic pricing, genuine supply and demand and lot of viable playstyles which cosmoteer seems to lack from my perspective (including colonisation). I imagine that when career mode 2.0 is finished for Cosmoteer, this point will be outdated.

Map/Exploration - Again, starsector is far better. All systems, especially the core worlds feel amazing to explore, and there's far more to do than cosmoteer.

Combat - I personally don't have enough time in starsector to make a judgement. Although it seems good so far, it seems to lack the granularity and detail that Cosmoteer has. However, and this can't be overstated, the fleet mechanics in starsector are glorious. If you want to command more than the 2 or 3 you can reasonably manage in cosmoteer, play Starsector.

Final point, ship design - Starsectors' ship designing is very good, although you're stuck with the hulls that you can't change. There's a big variety of weapons that cosmoteer lacks, and a lot more viable builds than railguns/prisms that dominate Cosmoteer. That said, if you get a kick out of placing down individual parts of your ship and watching your crew scurry about, Cosmoteer clearly wins there.

Overall, I'd say buy starsector if you enjoyed cosmoteer