Both are great motors. The BB will make over 250whp with a Profec B, JWT ECU, and Cobra MAF at around 15lbs of boost. The same setup on a GTi-R will make in excess of 280whp at around 18lbs of boost. Plus the GTi-R is a hell of a lot cooler to look at, what with the 4 individual throttle bodies an all!!!
Thrillseeker is right about the parts for the GTi-R. The water pump, oil pump, piston pin bushings, main and rod bearings, exhaust valves, exhaust valve guides and seals, rocker arms, valve spring shims, valve lash shims, entire intake, turbo.... etc.... all of these parts are unique to the GTi-R. Gasket sets were just (very recently) put back into production. The water pumps are damn near impossible to get ahold of.
Keep this in mind. I know people that have been waiting for over 6 months for a water pump. The BB shares all of these parts with the US SR20de... with the exception of the headgasket.
Both motors are great, as I said, but the BB is much easier to maintain as a daily driver. Believe me, I have a GTi-R in my '91.
PM me if you want more information.
Nick