If it suits all your needs, go with it. There are still some issues, but not as many or big as the X5. The X5 is essentially built on the E39 platform, while the X3 is on the E46 platform. I just wish the X3 was available in a V8, or at least the N54 tt motor from the 135/335/535/X6...It just doesn't have the sport options of the bigger SAV that I like.
Look around on the X3world forum, that should give you an idea of what people have been dealing with