Well, I'm about 3 hours into the first run and I have to say that there's a lot going on that I know I haven't found yet. I've stumbled across a few new colony items but nothing too "out there."
The bar missions are a welcome addition. Not only does it feel like there's 1-3 at just about every colony, I can tell there's very obvious consequences to many of them. Kill a Tri-Tach patrol? Hostile with Tri-Tach. Put a spybot next to Sindria (yeah right!), you'll need stealth. Then there's these weird missions about dropping bio-specimens in the middle of nowhere for decent coin. Surely that's not going to do something sinister, right...? The ones that have bit me so far are the "supply 3 Domestic Goods and I'll pay you monthly." I didn't realize I needed a colony first so those were instant fails. I really don't think those should even be offered until your first colony is up.
Story Points are very interesting. I don't mean to horde them but I had like 16 just floating around because I was accumulating them faster than I felt I had reason to spend them. Recently, I've been adding hullmods to ships and I've used them a time or too to get out of a bad fight but I haven't really leaned into them very hard yet. They still feel precious, despite knowing I'll never "run out."
The skill revamp is quite good, so far. Truly meaningful choices though the Elite Skills aren't quite as punchy as I originally thought. The one at the end of combat (which improves ship systems) has "+30 seconds deployment time." Great for a Frigate, I suppose but I'm already piloting a Fury and I'm still in the early game. I just don't think that "Elite" skill is all that Elite. Also, going back through the whole Combat Tree and grabbing Fighter bonuses (when I will likely never pilot a carrier) feels a little hard to swallow. I'm not sure if should be possible to "skip" skills in a tree using Story Points but I think I'd prefer that over getting skills I know I'll never see much benefit from. I think I understand the rationale but like "empty" Aptitude points in the last patch, it kind of feels empty (even though it isn't).
Btw, the Fury is a nice starter ship. I purchased one from the black market probably 40 minutes into the run and it's been fun. However, I'm discovering its limitations in raw damage output. I have a Ion Pulser and Phase Lance along with a Reaper in the missile and 2 IR Pulse. Maybe if I could find some Heavy Blasters it would open up for me but the damage is very anemic against Ventures and Enforcers. (Enforcers are true bricks now and I love it). I say this because I think the Fury would be a really good "high-tech Fast Start" kind of option with an introductory malus (kind of like when the Scarab was an option and you were hostile with Tri-Tach to start). An undergunned Fury (maybe 1 D-mod), a TT Brawler, a TT Buffalo and a Dram.
Gah, a lot to be proud of here and I've only scratched the surface. The dialogue is great, too. Oh, and the Gates tab...oh my.