Looks at the GT500KR's, people were going nuts over them and they've lost a ton of value. When regular GT350's fall in price over time, there's going to be a point where the R just isn't worth "X" amount over a regular GT350 to a lot of people IMO.
I agree with stanglife, that to me much of the significance of the GT350R was a radical leap in the direction of truly raw track performance that was more in tune with the philosophies of the older M cars, thus drawing attention from Porsche and BMW M fans such as myself. I certainly don't intend to offend other Mustang owners, but as a deep in the blood M and euro track car lover, I had absolutely no interest whatsoever in any mustang prior to the GT350R. I never saw the appeal of the GT500, and would rather have had many other cars in that price range. I would take an E92 M3 over the GT500 any day. If one morning I woke up to find my boosted E36 M3 replaced with a GT500 I'd cry my heart out. But now, I don't think there's any car under $100k I'd take over the GT350R, which is why I branched away from M cars to find one.The 500KR is the most extreme example and IMO, the worst cash-grab ever. It was a name and IMO pretty ugly and in-special. I knew right away those wouldn't hold their value.
We're talking about a car now that attracts Porsche owners due to it's unique characteristics. It's not going to become irrelevant anytime soon.