Here are a few major changes as best I recall.
1. Alliance system: alliance leader = war leader. Huge change, very important, and IMHO very good. Now you can successfully defend AI minor allies among other things.
2. The new straits added somewhere in the 1.08 betas are now moddable, so you can keep them or edit them to your own specifications. And you don't have to be a tech genius to do it -- even I did.
3. Somewhere in the 1.08 betas you lose 1 centralization after annexing a country, and fortunately that penalty was removed in 1.09.
4. Both trade agreements and embargoes now are very costly to your trade efficiency, 3% for each one of either type. Essentially TAs are now forbidden apart from perhaps one or two. Monopolies, though, are very sweet, now adding 2% each to trade efficiency.
5. Tech costs and merchant success both were made a bit worse in a presumed attempt to make the economy more challenging.
I've only played one complete GC under 1.09, with another about 1/4 done. So my experience is not vast with 1.09 but I like this version very, very much.