Played both last year (own the GW version) and enjoyed both but probably prefer (just) the GW version ... but with only a play of each that doesn't really count.
I don't like the 50/50 Day or Night chance in combat - in the GW game we played Drac was killed in his first fight because he rolled day and the Hunter had a stake. I prefer the time 'counter' in the FFG version as it gives both sides a bit of strategy in planning their moves/combat - I think I'll probably scan it from my mate's game and use it in the GW version.
And I don't like the VPs in the FFG version - especially for Drac for just surviving a few days. Our FFG game was quite boring for me, as Drac ran most of the time and won with most of his VPs from surviving and I never got near him so never had a combat.