I've had some long save time problems... but I think mine are mostly that there are some serious memory leaks that progressively slow down everything (including saving and more critically mouse response) after a few turns.
Saving, quiting and restarting speeds everything up for me, including save times.
"We found the problem and fixed it. The problem is that there are hundreds of combat log message being added to each of the computer players. Since they are all allied, and they all share combat reports, each one was getting a report for every other player (11 players x 11 players). The game now checks to be sure that you don’t already have a combat report for a specific battle before adding a new one."