I drove both of them - the X1 is my favourite.
The 3 series offers more room and the quality of some interior elements is better than those in the X1. But overall I prefer the X1 because of its look (compared to the 3 series it looks much more exciting to me) and the higher driving position. Technically the X1 is based on the 3 series, so it's basic qualities and driving abilities are pretty much the same.
In my opinion the X1 is great alternative to the current 3 series.
But it's all a matter of personal preferences.