I only know about the E85 (2003-2008) from info gleaned from the Z4 forum as never owned one. Others will be more qualified.
I have had two E89s and the consensus with them is this IMO:
They are generally more 'grown up' to drive than the E85. Heavier, more GT than sportscar but are much more refined and 'modern' feeling. They have a folding hardtop roof which makes them good for year round use, but the roofs are very, very complicated and can be costly if they go wrong. Personally the only problem I have had is microswitches in the rear which cost pennies and an easy DIY fix!
Early 6 cylinder engines (N52) are reliable and good for high mileages if looked after. Those were fitted to the 23i (2.5 litre) and 30i (3 litre).
The 4 cylinder 2 litre turbo (N20) was available almost through the entire production. It came in three variants; 20i, 28i and later as a very detuned 18i. The engines are all identical, except the mapping from the factory. The 18i and 20i can be cheaply and reliably remapped to 28i figures and beyond (250bhp and 320nm). They are good engines but there is a slight question mark over camchains, as these can wear prematurely.
The highest performance engine in the E89 was the N54, a 3 litre 6 cylinder twin turbo (not to be confused with a 'twin scroll' turbo which the N20 uses). This was in the 35i and range topping 35is. Big power and speed but there are major question marks over reliability with the N54, as they have a nasty habit of breaking very expensive components (like turbos and fuel pumps, etc). Great fun when they work, though!