Things that changed:
The speed 0 crit is gone, replaced with adrift.
Certain crits no longer include no special actions as part of their effects.
There is no longer any 'no wepaons' crits.
You can lose traits through crits.
Crits are easier to repair with 'All Hands to Deck'.
Anti-fighter is now a reactive trait.
Escorts add a new wrinkle to the game.
Admirals for every fleet.
There are two new fleets (three if you count the pak)
There is new stuff for every race.
The Centauri fit what we see in the show better.
The fleets and ships are generally more balanced across the board.
Armageddon ships that were lacking have been given a big boost.
I heard that Mongoose pulled the usual and just fixed the stuff that was already ok and ignored the stuff that was way out of wack; no real surprise if you ask me. Too few are the full blown corporations that listen to the masses...though I couldn't tell you why that is.
Don't believe everything you hear.

Mongoose hardly fits the description of 'full-blown corporation' and a lot of the things that got changed in 2e got changed because they were asked for.