X1 lacks a lot of aspects of the 3 current series. The X1 is based on the old 3 series wagon E chasis and though the X1 is "new" to the US it's been around for 6 years in Europe and the current chasis is near it's end of life, probably MY2015 will be its last. If you compare even standard features of the two you'll see the X1 lacks about 30% of what the 3 series offers. Many standard and optional features in the 3 series aren't available to the X1 because the X1 wiring and technology can't support it or because the technology came out after the X1 design was finished and are too major to add mid cycle.
Outside of comfort, the 3 series has a much more finished interior . The X1 is a lot of plastic and just not as refined. Passengers in a 3 series can enjoy options like rear heated seats when the X1 doesn't even have an AC vent for the back seat.
The X1 costs less but you get a lot less. X1's are great for performance in a slightly higher ride height but if bells and whistles and comfort are important the 3 series is often the way to go.