1. Kineticist class got added, as well as Psionically-Attuned Staffs and a Kineticist-Exclusive Psi-Noise Generator Accessory on Zheng Shi. Broken Psi-Amp cannot currently be repaired, but it's on the To-Do list.
2. Dhaal's dungeon has been added. The loot at the end depends on who you sided with at the Party, but you can exchange it (once) by going to a certain area of Gabtown.
3. A new planet, Phaedra II has been added. It's under heavy construction.
4. Level 12.
5. 'Flying' is now a status Steele can have. It makes basic melee attacks and most ground-based Trip attacks auto-miss. Unfortunately, most enemies use melee-themed special attacks which ignore Flying. Flight-Capable Wings and the Light Jetpack grant an activatable ability instead of being passive.
6. There is now a Species Selection menu in 'Appearance'. Only those above a certain threshold will appear, but you can now resolve close conflicts manually.
7. Deep Freeze got massively nerfed but is no longer exclusive to the FZR Fire Suppression System.
8. Steele has two separate stalkers. Fortunately, they're optional.
9. There's an Autosave feature. You can set how frequently it saves, or turn it off.
10. Zheng Shi Ops deck has been added.
11. The procedure for sneaking in on Zheng Shi has been changed. You now have to either fix the elevator yourself, or hand the Spacesuit Helmet to a pirate at the Airlock. The Slave Suit has been moved to the Pen.
12. Bulky Belly can be negated with the Thraggen Harness, sold by Inessa.
13. You can click on the map to auto-walk there, assuming no random encounters.
Plus a bunch more character expansions and items.