Bah, Paradox games always slow down the further along they get. That's par for the course. It's to be expected. If you can't handle it, don't play Paradox games.
Now, having said that, there are some things that will help. I have also noticed that the next to highest speed setting runs a little smoother, so that's something you can do. I have also noticed that marathon play sessions don't help...so take a break, exit to desktop, go get a drink, reboot and things should be running much smoother. Also, I'm sure Paradox will come out with a few fixes here and there, tweaking performance. I have also gone back and played older games, such as Vic1 and CK on newer machines and they do run quite a bit smooother.
With games as complex as Paradox puts out, I'm more amazed that they run at all, at any speed. The sheer amount of data processed is mind boggling. Pop demands, moving AI armies around, calculating daily fluctuations in tax revenue, calculating interest on loans, deciding whether to pop a random event today or tomorrow, managing the world market, etc etc etc etc. All of these games, from EU1 to Victoria to Crusader Kings to EU3 to Vic2 are probably some of the most sophisticated and complex world models that have ever been put out, outside of government think tanks doing weather system simulations on IBM super computers or something. And they run on standard home PCs. That's pretty awesome, if you ask me.