It is a downscaled version of the original Prometheus. It is not like the Avenger in any way, because the Avenger could still be put to good use even after the introduction of the Prometheus. The R, however, can hardly be put to any use, even before the production of the Prometheus S.
According to Intelligence in FS2's tech database, the Prometheus needed argon, a gas found only in Sol, in order to work. Because the Lucifer's destruction collapsed the Delta Serpentis-Sol jump node, the Alliance had to improvise. They made the Prometheus R using some of the technology that powers the Banshee, but they didn't do it very well. The Alliance eventually found enough argon in the nebula beyond Gamma Draconis to create a proper version of the Prometheus, distributed as the Prometheus S.
If you need statistical evidence, the most damning one is the refire rate of both weapons. While the Avenger and Prometheus R do around the same damage per shot, the Avenger has twice the refire rate of the Prometheus R, meaning that it does about twice the same amount of damage as the Prometheus R should all your shots hit.
The Prometheus R is not a newer version of the Avenger. It never will be. Anyone who says otherwise is calling me a liar.