I owned an FJ Cruiser (traded it for my current 4Runner), and currently own a BMW 545. There is no comparison between Toyota and BMW. Completely different animals for different styles of driving. If your wife is only used to (and likes) the BMW style, then the FJ will be a radical difference for her. If, on the other hand, she likes offroading and higher vehicles that are rather heavy and sluggish as compared to the BMer, them maybe she'll love it. Personally, I'd let her decide.
ETA - Since I see you'll be the one driving the FJ, then I'll add that the 4Runner is a step up in my opinion from a "civilized driving" perspective. If you're an avid off-roader, then I give the FJ the edge. The FJ is not nearly as nice to drive through town or on the highway as a 4Runner is. Most of the reasons have already been mentioned, but I'll also add "road noise" to the comparison. the 4Runner is much quieter than the FJ, and the BMer is FAR quieter than both of them.