I agree on the engine changes, that's made a big difference. That removed alot of moldy cheese from the game o.0
The campaign is outstanding. I never really got into the first GalCiv...I liked it, don't get me wrong, but I'd play it for a few days and just get bored with it. I'd go back and play for hours in the ship designer trying to re-create a ship I'd seen in a movie or something.
As you can see by the number of posts in the show your ship designs area, I haven't had much success in this endevor

Anyway, the new campaign is really execellent, however I was disappointed that the Krynn were not introduced at some point. I thought they would be a major plot device somewhere, but it never materialized.
The ship designer got a big overhaul, and every race got an extra hull to play with in each ship class. Some are hot, some not-so-hot, but all in all it's definately cool. With Kryo's mod, it's even better (but that's just cuz I like seeing all the hulls available even if I never use them). There are also some new and cool ship templates--actually, alot of ship templates, and for each race and ship class--so you've got some cool ships to play with from the outset.
The espi system...well...I could take it or leave it. I can definately see how it could be a decisive factor, however it hasn't been yet in my games. It can get darned annoying when lots of civs gang up on you with agents but that's the way things go sometimes.
I definately like the combat update, now ships with multiple weapon emplacements can target more than one ship per turn. Now you can destroy cannon fodder fleets in one turn if you've got enough weapons (or few enough enemies)!
Mega events are cool. I've seen quite a few cool ones, and I'm sure there's many more. That alone keeps me playing sandbox mode.
If you're a fan of pirates, they got a big boost in DA. They spawn in good sized fleets of powerful ships, and they seek out and murder trade routes. Mercilessly. Generally the ships are of high enough quality that they easily equal or exceed the combat power of a typical ship-of-the-line of the current tech/era/whatever.
I had an end-game pirate fleet consisting of about...8? tiny or small hull ships accompanied by 4 medium sized ships. Here are some numbers from this fleet: Beam Defense: 367+; Point Defense: 200+; Armor: 450+; Beam Attack: 0; Missile Attack: 1024+ (!!!); Mass Driver Attack: 300+. That fleet pretty much removed my navy as a major threat as my most massive ships were all spaced by them. It seems that whatever weapons they had were either much more powerful than mine, or much smaller allowing them to mount more. When I got down to just a couple of the mediums, the missile attack numbers were much much higer than my Huge ships mounting blackhole eruptor missiles along wtih some defense. Thier defense was even higer than my huge ships, so those pirates must have got thier hands on some serious tech. I'm not sure how that happened, but I just take it in stride as a game mechanic for helping me upgrade my navy