Well the facelift 2.5i is just a restricted version of the facelift 2.5Si, so it seems a bit pointless really as you'll get exactly the same running costs without the performance! (I think it was intended to replace the pre-facelift 2.2i).
Personally I'd avoid any 2.0 model as it's a 4 cylinder engine, and a straight 6 is one of the Z4s more unique features. As well as giving performance more suited to a sports car, a straight 6 also sounds better!
But then maybe I'm just too much of a hooligan - I just replaced an E91 325i with an E90 330i because I found the 325i a bit gutless!
Anyway another bonus with facelift models is they came in 2 trim levels, SE and Sport. BMW typically confused everyone by calling the seats in the SE "Sport" seats, but calling the ones in the Sport models "M-Sport" seats. M-Sport seats are very desirable, with used pairs selling for the best part of 4 figures so retro-fitting isn't really economic unless you get the car dirt cheap. I've put a photo of an M-Sport seat at the bottom - they just seem so much better suited to a 2 seater sports car. They were an option on facelift SEs and all pre-facelifts, but not an option too many people chose!