Being an owner of both TDIs and a 2.5l I would say the following:
1) In vermont my outside storage for the TDI gets -35 to -45 below with wind chill and very few colt start issues are had as long as the car is used within 8-12hrs time period (if it sits longer in that weather I like to have a block heater on)
2) the 2.5l is arguably one of the most reliable motors out by VWOA. Talk to any service rep and they will tell you they see 2.0T cars, 2.0 CRs, and then lastly the 2.5L for warranty and service work. Many will tell you the timing engines just run.
3) The 2.5l is a fuel hog in comparision to other 2.5l cars on the market and has slightly less power although these cars with a tune and basic mods are a blast to drive.
4) The tdi has loads of torque, in my opinion commands better MPG from the driver and is the car of choice for long travel
5) Replacement costs on the 2.5 is lower than the 2.0 CR TDI
6) The 2.0 CR TDI can get an avg of almost 10mpg more than the 2.5l on premium fuel. (the 2.5 likes 91-93 octane fuel, The 2.0 likes EU diesel or fresh diesel with a good additive)
In my opinion it depends on how many miles a year you plan on putting on that car. If <= 13000 a year then go with the 2.5 If >=15000 a year go with the diesel The inbetween is a crap shoot, the diesel pays out in higher mileage vw the gas pays out in low to average mileage range.