Well, I see your apprehension in having a iPhone and a theatre version of your movies, but really, with any decent computer, especially one that collects large high quality movies, hard drive space and organisation shouldn't be an issue. Plus you can convert 1080p to iPhone native h.264 in real time and a 2 hour movie is probably only about 1gig.
As well, how much faster is transfer to the 3GS? I was syncing a different season of a TV show (about 4 gigs) and it took like 30 minutes on the slow 3G memory chips.