I'm not convinced any of the new weapons are better than Missile Turrets. More specifically, I'm not sure they're better than the two Missile Turrets I was using before. They're mostly more specialized, so it might be optimal to have, say, a Tachyon Lance and a Relativistic Launcher and use the TL vs Shields and RL vs Armor, but two MT have better effectiveness vs Shields as the TL for better Energy efficiency and they're about as effective vs Armor, so you don't have to bother switching weapons.
I do like the idea of a ship with just the Tachyon Lance and a bunch of Drone Swarms. The better combo in testing is the Relativistic Launcher + Drones. The Drones do Electric, so they shred Shields, while the RL does supplementary damage, and then they reverse roles vs Armor.
Logistics Suite makes having a variety of Gadgets more viable, but I'm not sure how many uses you really need.
The biggest addition is probably the improved Crew Quarters, so you can fit more modules in for a given number of followers.