I recently upgraded from 1.x to 2.x and everything worked almost seamlessly. Plugins won't have to be updated unless you want to, and their settings should all transfer fine.
Most of the changes are cosmetic.
As theducks mentioned, you might see some new icons. If you don't like them, you can install a different theme. Unfortunately, you can't get back the 1.x icon theme.
The close buttons on the Virtual Library tabs are a little annoying. I switched over to the dark blue icon theme so they wouldn't be as visible, but as far as I know there's no way to turn them off.
The height of the rows in the book list has been increased. If you don't like it, you can change it with the "Extra spacing between rows" parameter under Preferences -> Look and Feel. I found that a value of -11 seems about right to set it back to the 1.x row height.
Aside from that, you shouldn't notice too many changes. The rest is new features that aren't in-your-face.
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