There's certainly a lot of changes that have been made to the game, but they definitely feel consistent with DL if you played that a lot.
I am in a similar position as you having just come back to GalCiv by buying the DA expansion. I had been playing DL still fairly regularly but hadn't looked into the workings of DA until I bought it.
For me, the most integral change is the colonisation element of the game. This is due to 2 main changes/additions.
1) The cost of colonisation has increased dramatically so that you do need to be selective and strategic about your initial colonisation process - this is a definite pro and adds a lot to the early game.
2) Extreme colonisation really adds long term depth to the game. It is common even late in the mid game to find absolute jewel worlds uncolonised because the AI has failed to achieve the necessary tech. The highest I have found in my game is a PQ 27 Radioactive planet sitting in the star system next to the Korx homeworld. Jaw dropped, fingers trembled as they found the nearest planet and rush-bought a long range coloniser!!

Yes, the new races and new super abilities are excellent and again add strategic depth, but colonisation is the core to the game and these 2 developments have had the most impact on the game for me.