If I'm going to choose one over the other, it has to come down to which I enjoyed more on the initial, and subsequent playthroughs. Which means the winner is far and away, the original RB games. While FRLG did obviously fix a lot of problems and looked sleeker, nothing about playing those games stands out for me. They didn't do enough to capture (or recapture) my imagination and joy. I still have many memories of playing Red for the first time almost 20 years ago, while I have practically no memories of Fire-Red. So since in my mind they are virtually the same game, if I'm going to replay one of them, I'm obviously going to play the one I had a better time with.
Also, while it's not the original question, I always preferred having my GBC than the Advance/SP. Obviously the latter two were better devices, but I liked the feel of the GBC more. So that also influences my decision. Even though now of course I would be replaying on the 3DS.