For long run (for example: 100,000+ miles, 6+ years), I will recommend manual transmission. It has much longer life than automatic, has better mileage, you control the power of the engine, control shifting, so on. But you have go through headache of shifting, specially in start/stop traffic.

 

This is all speculation based on no hard data to prove one is more "durable" than the other. Until such data is collected and analyzed as to whether the Aisin is more "durable" than the Getrag, well, choice will only be made on personal preference.

I chose the auto because of multiple defect issues with the LuK clutches and flywheels on my R53 (two complete sets in 27K) and that I have a bum arthritic left knee (old ski accident) that will require surgery soon. For me, while clutching is a VERY painful process I'd rather not endure, I am not enduring any less fun with my 09 auto than I did with my 05 manual--a MINI is a MINI, fun-factor wise.

I know lately there have been reports of Getrag mechanical failures on 09s with very low miles, and there have been instances of the Aisins needing to have their adapatations reset. Ive not heard of any major mechanical malfunctions on the Aisin, just software bugs every now and then.

A non-MINI example: my friend has a 2000 Chevy Duramax Diesel PU with the H/D Aisin 5-speed automatic truck tranny and it has held up very well over 125,000 miles of trailer towing and hard hauling over 11,000 foot high mountain passes, with only one fluid change at about 75K. Still shifts as smooth and precise as the day he drove it off the lot. And my Toyota mechanic swears by Aisin as the best auto tranny manufacturer in the world, mostly because QC is taken very seriously in the Aisin corporate culture.

Still, MINI-wise, the potential weak link with the manuals aren't the Getrags, but the very spotty LuK clutches and DM flywheels the Getrags are connected to, something that's not an issue with the automatics. To make matters even worse, there are some MINI dealers that will attempt to blame a clutch or flywheel problem/defect on "operator error," and deny warranty repairs. So keep that in mind as U flip the coin, if y're on the fence here.

 

This right here, FTMFT.