I kind of hate to start this critique off with some negatives, but I am going to, because it's important to give it straight. Overall, I like a lot of the changes. The game definitely feels more finished; there's more good than bad here.
1. The new skill system. Man, IDK. On the one hand, skills matter a bit less overall; this is probably a good thing.
However, the way it's set up is... weird. There's no flex, it's all about being in the right pigeonhole... and the 15 levels mean you can get 37.5% of the total skills.
Soooo... all the skills need to be pretty amazing, frankly (or equally meh). I already dislike the, "you can only pick B if you've taken A in the chain" mechanic; it's even more irritating than the, "burn 3 points to be able to max any skill" in the old system. It's almost the epitome of how to make an open-world game feel restrictive.
If the fifth items on each chain were amaaaaaazing capstones, it'd at least offer a reason for this, but that's not how it works. I mean... case in point: Missile Specialization is one of two capstones of Combat? Really?
The flavor texts are also an unfortunate example of where that's not actually a good idea. They simply aren't very informative, and new players will be confused. I get what you wanted there, but the right answer is to describe the general mechanics, then provide some flavor, not the other way 'round. The mechanics, meanwhile, are in teeny-tiny script that's dark and hard to read.
Lastly, the "oh, but this doesn't work if you have X FP of Y stuff" just gives me a headache. I get why it's there, the whole, "try and limit player power in a soft way", etc., etc. and that's fine, but frankly... it's just un-fun to read it and try to understand the mechanics.
So... buying skills has gone from a moderately-annoying exercise in choice anxiety to "wow, I need to whip out a calculator and read some forum-dude's calculations about how to use it, and then build to a precise meta", and I'm not honestly sure that's an improvement, despite the obvious amount of time that went into making this system.
Like, if this was the goal, why not have explicit character classes? Because this amounts to a class system, only with a rather confusing presentation.
2. The Hard-Flux Beams; 50% range on a PD Laser means that it's basically not a thing now, and Tac Lasers are... uh... 500-range weapons that trade 1:1? Wow, sign me right up, lol.
It's a cute attempt at a tradeoff, and frankly it's great that Beams finally got some love... but this mechanic might need some work. Also, the OP cost is like, "whaaaaa" for what you get. At 1/2/5/10, I would at least think about it (and probably be disappointed).
3. I really like the Assault / Escort Hull Mods.
4. I think the change to the Annihilator Pod is very interesting. I'm not sure if it's good or bad, but it's interesting that it's basically a flux-pressure hose that mainly eats the opponent's Soft Flux reserves, rather than doing real damage. David's rework of the art is nice, too. Heck, the work on the art for this version, in general, is really nice.
5. Is it just me, or did Talons get a buff? They felt rather vicious against Pirates. I mean, I'm OK with that; Talons should be worth their 2 OPs, lol.
6. It looks like System Bounties were increased a bit. Thank heavens, they're almost worth doing now.
7. The perma-mod mechanic is really cool.
8. The "miracle worker" mechanic is also really cool, and will be heavily abused to farm rare ships and weapons mounted on same, lol.
9. I haven't even done any of the new missions yet, but I know I'll enjoy them. Knock out ports for Pirates? Sign me up.
10. The mercenaries are... interesting. I need to understand the new Officer limits, but if they skirt those, they'll be actually useful... but frankly, I'm expecting a lot of them to not be, because they don't have the right combination of skills to minmax their meta pigeonholes. This feels like a Newbie Trap, frankly. Maybe they'll turn out to have rational hard-wired sets of useful skills rather than RNG; I haven't stared at enough of them yet. But the one in Galatia was kind of a mixed bag and I passed her up.