Someone might have more insight but here's my thoughts in short.
Both X1 and 3 series wagon use the same xDrive so there shouldn't be much difference there.
The new wagon willl be based on a new chasis (X1 was based on the e91 wagon chasis) but off roading I can't see much of a difference between the two chasis. Some F chasis BMW owners liked the e90 chasis more, some like the new, it's a mixed bag but that's for performance/track handling.
The 3 series wagon will have a nicer interior than the X1.
The X1 looks more offroad willing.
The X1 does have clearance as you noted, and that doesn't matter for off roading but to be honest I think it's really
So in short, the only difference is interior and exterior looks and the X1 has more clearance. Oh, the 3 series wagon will have a bigger boot if that matters much but again, it's not something that helps for off roading.
I'd say consider the X1 over the 3 series only for the ground clearance as it might come in handy on BLM and back roads once in a while. The 3 series should be fine though, but you never know how big of dips and ruts you'll get on BLM land so more clearance might save you but you could as easily find the X1 unable to clear some land too.
3 series will perform better on non off roads though.
Last edited by edx1; 11-17-2012 at 07:21 PM.