Wait till iBooks 1.1 is out before making an opinion about it. We have no idea what's included for the PDF support. Does it support bookmarks, notes, highlighting? Readdle may be able to support those features that iBooks may not.
I'm guessing that you'll have to sync the PDF's via iTunes, which makes it less convenient than apps with built in transfer functions like GoodReader etc - unless Apple remove them from the store of course