I have an EX-3 and edit native files exclusively. It works great. I think if you change to Prores it will take forever to render to that codec and it could be a LLLLOOOOONNNNNGGGGG time before you got down to editing if you had a large project.
Again, I edit in FCP using the EX easy setup and it works great. I then send to compressor to get it ready for DVD or web upload. I will sometimes export with Quicktime to make a Prores file if needed.
Apple Certified Master Pro FCS 2
Sony EX-3
MacBook Pro