Its an interesting comparison. The basic 944 turbo is 250hp, the base MR2 is 200. Typical used car prices are about the same right now. However, the bottom end market prices probably represent neglected cars. IMO I think an MR2 can emerge from this history of neglect cheaper than a 944T.
I've read that 944's are prone to water pump problems that can destroy the timing belt and the motor. The 944 2.5 liter engine is an interference engine so timing belts must be replaced regularly. The Porsche specific tensioning toll used to be ~$400, but I have seen cheaper knock off on ebay recently.
Porshce clutch jobs are crazy expensive. The 944 tranny is in the rear and because of a funky torque tube design I've read the clutch labor is high.
Anyway, like Jekyl said I am biased too ;-)
Aaron
www.atsracing.net