For one thing, with Prism, binding events to view model methods was a giant pain, specifically if you wanted to pass event args. I know I ended up having to write a number of attached properties to handle different event binding scenarios. With jQuery it's a cinch to handle user interaction. (I guess my major gripe in this case is with Prism, which is perhaps separate from SL).

Further, text wrapping and layout were my biggest pain points in SL. I wasn't used to having fixed dimensions on everything. That really bugged me.

Finally, I didn't like the visual state manager at all. There's not really an analogous equivalent in JS/HTML, but for a "rich" internet platform it certainly didn't seem like the way to go to me. I have to run now, but I'll try and think up some more of my pain points and edit as appropriate.