Actually, I was thinking R/T almost exclusively from the start. BUT....
now that I look at how much more you get with the SRT (premium suspension, better interior, better exhaust system, 180mph speedo, more standard equipment, better upgrades, etc.), and considering the minimal difference in price once the R/T is similarly equipped, I'm leaning much more toward the SRT now.
Both will require premium fuel, so the fuel savings cost difference that was there before is virtually gone now. The car HAS to have a manual for me to buy it, and neither the 5.7L or the 6.1L are offered with MDS on the manual...... Where's the allure of economy with the R/T now? I'm further betting that the R/T will have "some" sort of gas guzzler tax on it as well since the base mileage is improved by 7%, but loses the 20% benefit of MDS, setting it closer to the SRT overall.
Even if the original buyer has little/no intention of getting a Challenger as a collector's item, someone further down the line will wish it were bought and treated that way.

Look at the differences in price between the 1970 Challenger R/T with the 426 HEMI 4 speed, and the 383 magnum 4 speed. While both are VERY stout performers, highly prized by collectors, and probably wouldn't be used to their originally intended potential, the 426 HEMI is THE collectors' piece and commands a (substantial) premium at auction.
In retrospect, the difference in purchase price between the 1970 Challenger R/T with the 426 HEMI wasn't much more (in today's dollars) than the 383 Magnum or the 440 six-pack, for that fact. At the time, it was substantial, but not now. And the difference in "value" now far exceeds (in percentage) the difference when new.

Yeah, I'm thinking SRT now - keeping it stock until it's paid off. Then maybe I'll put some chrome valve covers and engine dress up pieces on it (braided stainless steel lines, anodized couplers, etc...). But this is going to be something I have and keep until I'm worm food and HAVE to pass on to the kids. I want to get in, turn the key (without bloody knuckles), and drive as-is and have a blast doing it. I'm thinking it's gonna be an '09 SRT now.