The patches balance out some things, fix some bugs, and beef up the AI (as well as mod support). I don't know where the choppiness comes from, the patches work just fine for me. But other than adding the Unfair AI they don't add new things to the game, so you can do without if you don't want to play mods.

You can also try the 1.1 beta (1.09). The devs optimized the engine even more and according to several posts, it does work quite a bit better in general, so maybe this patch will solve your issues also. To get it you'll need Impulse, click on the blue orb in the top left and check "Show pre-release versions".