Hi vjmvjmvjm,
I went for a test drive before noticing your post and my impressions from the test drive are same as yours. I'll even go as far as to say I'm both pleasantly surprised by the pep of the sport wagon (note I'm no longer using quotes for "sport") and disappointed by the GT.
For my test drive, I drove the only wagon they had on the lot -- 328d (diesel). My, what a surprise. As you wrote, handling characteristics and acceleration are comparable to any 3-series sedan and favorable overall.
The Gran Turismo 328i xDrive AWD (4 cylinder) was my second test drive. If I recall correctly, it's the same engine as in my Z4 4-banger, with which I'm quite satisfied. As some of the online reviews say, you really need to put the car in Sport mode to get much acceleration or performance out of the vehicle. Even in sport mode, the car drove more like a luxury car than a performance car. Again, not a surprise considering the size and weight of the vehicle. The sales rep (Percy Covington, who I enjoyed talking with) stated that the 3 series GT is based on the 5 series chassis. The drive of the vehicle seems to support that assertion. Again, it's not that the car is bad, as control at high speed was consistent with the brand, it's just that I found the performance to be somewhat disappointing. The drive reminded me of a 5 or 6 series, and is not really what I'm looking for.
The data sheets say the GT has somewhat more headroom for the rear seat passengers and a bit more cargo space in the back than the wagon. I didn't really notice all that much of a difference. The slope of the rear window on the GT seems like it would limit the usefulness of the cargo compartment, but in the absence of actually using it, it's difficult to say there's any impact.
The other pleasant surprise I had (with both vehicles) was the rear-view camera, with stadia line overlays, and proximity sensors. I've driven other cars with similar features, but BMW's implementation is superior, in my opinion. The stadia lines overlay on the display to show you where the car is going, and the proximity sensors give you an audible warning as you approach other objects while parking. While it doesn't seem like much, the combination of these two technologies makes vehicles so equipped much easier to park. In fact, considering the sizeable blind spots in both vehicles, I'd say that the money spent is better spent on those features than on body work (been there, done that).
Now I find myself in the curious position of spec-ing out a station (um, 'sport') wagon because I like the drive better than a 3-series. Hmm...