3.0si is faster and uses less fuel seems like a win win if you can afford the extra. Also newer cars tend to have less issues than older cars another win.
Fox goes on about age in relation to E46 being a bad thing yet is advising to buy the older car with the older engine. Regardless the E85/E86 has aged very very well it still looks very modern. In fact ask a random person who knows nothing about cars and they all prefer the look of the older Z4 than the new one.
The N52 is meant to be less reliable but that's only because the M54 was bulletproof. Any engine after it would be less reliable because the M54 could last 300K no issues.
They are now up to 13 years old so people seeing EPS, suspension issues, etc. EPS to replace with a new unit is around £2.5K for the part alone. Some are now modding to hydraulic steering or replacing with second hand units, it's a common issue. So it may pay off to buy a newer model with the newer EPS system.