I don't like that subclassing generally doesn't work. You can subclass PFObject no problem, but you lose it when you are doing a lot of PFQuery'ing. PFUser would be a prime candidate for subclassing but that really doesn't work without a lot of shim'ing.
I don't like the lack of client side persistence. There is caching with PFQuery but it's caching the json response from the server. For example, let's say I have a message board with 1000 messages. If the user posts a message, I can't simply add the new post and have it cached, I would have to query and pull down all 1001 messages.
Now, I've written all the boilerplate around the parse SDK to do all of this, but it was kind of hacky. So now I'm ripping it all out and just using the REST API with my own custom digs. Much smoother. I'm slowly moving it over to it's own static lib at: https://github.com/jawngee/CloudObject
Don't get me wrong though, their SDK is definitely usable, but after a certain point it becomes a little cumbersome.