Trying to disect the price differences between cars/lines is an exercise in futility, since for the most part it's not based on the cost of materials, but rather on what the market will bear. There are much cheaper cars out there with a lot more standard features than any BMW. And 2-door BMW's cost more than 4-door ones, even though they used less doors to build them, so they should have been cheaper, right? I think the X1 is cheaper because it's not yet a well-established model, unlike the 3-series. Expect pricing to increase for the new X1 generation in a couple of years.
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