If you are at all unsure, buy the automatic. Problems will be resolved with updates. There are not transmission problems as much as there are a small number of programming problems IMO.

My dealer had approximately 20 X3s on the lot and in the showroom several weeks back. Not one was a manual. They remembered a lease return four months back, but hadn't seen another manual X3 for some time. We ordered a new 3.0si 6MT which is scheduled for July production. Dealer's main concern was that we would try and trade it in after 2 years.

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2007 X3 3.0si, 6 MT, Premium, White

Retired:
2008 535i, 6 MT, M Sport, Premium, Space Grey
2003 X5 3.0 Steptronic, Premium, Titanium Silver
2002 325xi 5 MT, Steel Grey
2004 Z4 3.0 Premium, Sport, SMG, Maldives Blue