Utility
Drivers with frequent child-duty might favor the Dodge Sprinter Wagon 2500 over the Dodge Sprinter Van 3500.
The Dodge Sprinter Van 3500 is a better choice than the Sprinter Wagon 2500 in terms of hauling capacity, especially if you often need to carry a lot of equipment or sizeable dogs.
The Sprinter Van 3500 outpulls the Sprinter Wagon 2500 by a sizeable margin.
Cost
With respect to MSRP, the Dodge Sprinter Wagon 2500 costs about as much as the Dodge Sprinter Van 3500 (though the Dodge Sprinter Van 3500 is a tad cheaper).
Warranty
The Sprinter Van 3500 and the Dodge Sprinter Wagon 2500 have the same basic after-sale protection.