I think it's a long time since they've put out a major upgrade like this (and they said it was complete rewrite, which I believe after using it for a couple of days), so I don't really begrudge them charging a modest upgrade fee. I find the new version much more intuitive to use and also "smarter" in that it seems really well designed for people who like to download binaries.
The one thing I don't understand is the auto unpar/unrar/join thing, which sounds great except I can't get it to work. The promo webpage for Unison 2 says "Built-in UnPAR/UnRAR/Join, no external tools needed." Almost everything I download is broken down with .par files yet Unison doesn't combine them after downloading; I have to run MacPar to do that... so either I'm not setting something properly or it's not doing what it says it will do.