One of the main reasons people swap out the torque tube is money. To rebuild the thing and install the 3:55 R&P is going to run you around $700 just for parts. From what I've been told (I restored my torque tube and did the R&P) you can get an newer open driveshaft unit for under a $100.
That's a pretty big issue to deal with.
Personally I'm glad I sucked it up and kept mine stock. I like the idea of having it that way.