If you're looking new, there are very few options out there; Elantra Touring and the Jetta Wagon are about it. Of the "wagon-like SUV's", the Outback is probably the best bet if the ridiculous roof rack isn't a deal breaker (for me, it is). Good fuel economy with either the CVT or the tall 6 speed MT. I just wish they still imported the Legacy wagon. Of the "big hatchbacks", the new Impreza and Mazda both look really good as well.
If you're willing to look a few years old, I'd add the Focus wagon and V50 to this list. In reality the Focus wagon is probably the only thing that really fits what you're looking for, and I think an' 05-'07 with the 2.0 Duratec would be perfect. Unfortunately, lots of other folks have the same idea...
Two other honorable mentionions that are wagon-like would be the Mazda 5 (before it turned into a small minivan) and Ford's Transit Connect. Nothing beats the TC for the space/fuel economy ratio, and I'm seriously considering it as a potential replacement to the Freestyle.
Lastly, I wouldn't discount a P2, '04-'06. It has a bit more space than yours, similar fuel economy and it has familiarity going for it. The first P2's had some well-documented transmission issues, which were mostly resolved by '04-and if you look hard enough, you can even find one in an MT.
If you trust the reliability of the TDI, this would be any easy call. Personally, I don't.