There may in fact be marginally more problems with a 4.4 over a 3.0, but I don't think it is enough of a factor to drive a selection decision. It is more about condition of each candidate vehicle, and then fuel economy and resale on the 3.0, vs acceleration on the 4.4.

If you like it, buy it. With both vehicles you should consider an extended warranty (if available) as repairs and parts aren't necessarily cheap.

Good luck.

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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