I'm on my 4th E89 and I've owned the N52 and N20 engines - for me the N20 was a mistake. I missed the sound of the six cylinder and despite the 2013 20i model I owned having relatively low miles I just couldn't get used to the agricultural sound it made.
Service history is often a problem with these cars because of long service intervals and the fact that the service history is often recorded on the key.
The other issue is the paint finish on the roof - nearly everyone I have owned has had this issue and although it covered under warranty you only have 12 years to get it sorted. It's surprising how many owners never got this sorted because they were either unaware it existed or were unaware of the warranty. Look in the cor ers of the top roof panel for what's appears to be snail trails under the paint.
When you check the boot for water ingress make sure you have a look under the sponge that covers the motor - as you can imagine it has the ability to absorb water so give it a good squeeze.
They all have headlight washers but often they can be disconnected so check those and while you're at it have a good look at the panel gaps between the bu per and the bonnet - same on the rear.
In terms of options the original catalogues are readily available in pdf format for years 2009 - 2014 so worth familirising yourself with those to determine what's available and what you'd like. Personally I preferred the absence of iDrive but phone connectivity and heated seats are a must. The upgraded stereo is a nice to have but depends on you priorities. Electric seats were only available as standard in the twin turbo models so most are manual but adjustment is good and if it's just you driving you will only need to adjust it once.
I'd mention also mention something which I've learnt from having multiple cars is that all MSport models have the anthracite headlining but it can be ordered on the non-MSport - it's only a small point but it does seem to age much better than the standard headlining.
The last point to note is that the MSport models were only available from 2010 and try to avoid the adaptive suspension - it will fail and it is expensive
My 1st - 2009 sDrive23i
My 2nd - 2013 MSport 20i
My 3rd - 2010 Msport 23i
Current - 2009 sDrive 23i