I had a '16 SS that I traded in December when we decided that we needed an SUV in the stable. (We rescued a pup that turned out to be part Great Dane.) So, I'm currently driving what was my wife's '13 Charger R/T --- that's the version with the 370hp 5.7 liter Hemi --- for the next year or two while I decide what I want next. Here's my opinion of each:
I bought the '16 SS during last year's 20% off sale in July (and picked the car up the night before the seat recall hold put cars on lockdown) and paid roughly $37K. Back in '13, we bought the R/T at roughly $29K --- car was $34K and there was a $4,500 rebate program on Hemi vehicles that Spring.
Paint quality is much better on the R/T. The SS had more chips when I traded it at 8,500 miles than our R/T has at 47,000 miles. And the R/T has spent a lot of time on vacations and country roads visiting my in-laws.
I don't have the panel misalignment issues or weather stripping issues that others have mentioned, but am aware that they exist.
The interior materials are nicer in the SS --- but there's no glaring "chrome" in the R/T. The seats are about a toss-up. A little better lateral support in the SS. Far more comfortable in the R/T. The back seats fold down in the R/T. The front cup holders are heated and cooled (very effectively) and the rear cup holders are easily accessible in the R/T. There's a proper coin holder in the console and plenty of room in front of the shifter for my iPhone as well as a storage area next to the shifter.
Our R/T has a sun roof and there's still room in the overhead console for a sunglasses holder and HomeLink -- which I gladly paid Snakey to add to my SS.
As others have said, the Uconnect infotainment system in the R/T is FAR superior to the MyLink system in the SS. The wonkiness of the MyLink system was a major factor in my decision to trade the SS on an SUV instead of trading the R/T. I'm a sales guy and work out of my car. The frustration caused by the MyLink and Nav system in the SS led to it finding a new home. I need things to work --- every time!
The exhaust sound from the LS3 in the SS is FAR superior to the R/T. One of the things that I really miss is the bimodal exhaust. I am considering changing the exhaust on the R/T .... just haven't found the "right" system.
The magnetic ride for the SS makes the car feel sportier than the R/T. However, the R/T is quieter and smoother around town and more comfortable on the highway. Even in '13, the R/T still had a LOT of Mercedes Benz in it and it handles MUCH better than you would expect from a car its size.
The fuel mileage on the R/T is much better than the SS and uses 89 octane versus 93. I routinely get 18-20 in the R/T around town (depending on traffic) versus 16-17 in the SS. On the highway at 78mph, the R/T gets 25-26.5 versus 21-22 in the SS.
The R/T has been very reliable in its first 47,000 miles. No issues at all. Just a couple of normal software updates. I did just do the brakes. My wife was side-swiped a little over a year ago and I think we missed a damaged front rotor during the repairs. The SS had the infamous high-side transmission failure at less than 3,000 miles and it took multiple trips to the Chevy dealer to get the seat belt and other recalls resolved.
Still ..... I do miss the uniqueness of the SS, the SLIRHM color, the extra ponies, and the exhaust sound.