In addition to the skill system changes, we had lots of other alterations we wanted to make after the beta. That is, after all, what the beta is for - to find things you want to fix or change, before it is too late. So we did that.
I don't want to list ALL the changes here, because frankly, I don't remember them all off the top of my head - but some of the bigger ticket items were to do with respecs and how we handle them, how we join games from friend lists, detection of low-ping players, and a bunch of other stuff. We made skills queueable, added Function key binding for skills, added inventory sorting, and so on. Justin spent a lot of time working on additional connectivity improvements and workarounds for funky routers. We also decided we wanted to put more work into our uniques to make them much more special, and so on and so forth.
We had some other items that weren't really finalized yet pre-beta that we wanted to get wrapped up too ( item recipes for item combination had some changes to how they function, for instance. We wanted more flexibility in how we could have items cast skills to aid in the creation of niftier uniques )
These changes all took time, of course, and we didn't get back to polishing the rest of the game until we were largely through with them.