There's quite a bit to this question...
2.5 vs 3.0 and pre vs. post facelift versions of both. As an example the post facelift 3.0 is nearly 200kw in a car a little over 1000kg so it goes like the clappers (a touch over 5 seconds to reach 100kms/h) and the torque is great.
The engines across pre and post facelift all sound pretty great. I think (* think) all the 2.5 and 3.0 variants come with the tube from the engine intake to the cabin to bring engine noise into the cabin. The 3.0 definitely do.
Do you want more speed and takeoff? - 3.0 (facelift = more)
Do you want great handling - both although the sports models include M suspension which works well
More bling? - the 3.0 have bigger alloys and some other bits; nothing major although a 3.0si or 2.5si include the MSports suspension. My 3.0si 2006 (facelift) also came with the M style steering wheel which IMHO is the best steering wheel I've laid my hand on ever, and to give you an idea I changed my steering wheel out twice in my BMW F30 and 3 times in my last MX5
The 2.5 and 3.0 engines are both great re fuel. The facelift option includes a better auto gearbox if that is your thing (it's great) and I get around 7 litres on average on long drives on the freeway with hills.
My daily is a twinscroll turbo 3.0 335 F30 BMW and the Z4 3.0si feels pretty closely matched, albeit not quite the same torque.
I went out for a drive with a fellow owner in a pre-facelift 2.5 auto and he was having plenty of fun
Just make sure you get a Z with the sports button if you have an auto!!