1. Significantly updated computer AI.  The AI is substantially better than in the current game. We're also evaluating whether to put in a difficulty level that gives the AI added bonuses since, in any RTS, a top human player will always be able to out think a computer AI. 
2. LOTS of new game setup options including:
   

   Pirates or no pirates in a given game
   Fleet size
   Income rate speed
   Build Speed
   Ship speed
   Research Speed
   Culture Speed

3. The open market for buying and selling of resources has been altered so that there are random fluctuations in pricing and can crash or boom based on player behavior.
4. Improved group phase jumping for large fleets of ships.
5. AI will surrender if situation is hopeless rather than drag the game out.
6. AI players will replace humans in multiplayer if a player drops.
7. Defeated players who are observing can no longer give resources or place bounties (bit of an exploit there).
8. Lots of tweaks to Ironclad Online for messaging users.
9. Improvements to network coding for multiplayer play.

Via Sins of a Solar Empire forums