Wasn't that pretty much the routine for every heel in WWF circa 1974-1989? Heel wins first match via CO/DQ, face/heel wins 2nd match in controversy, face wins 3rd match convincingly, moves on. Once SNMEs came on you couldn't do that as much, and especially once RAW started. But it's not as if Hogan started the three match series.
As far as the answer to the original question, since Hogan and Rhodes virtually never cleanly jobbed on TV (and I'm talking "1-2-3" in the ring no controversy) they are probably tied at 2-3 pins. Even's Andre's televised pins on Hogan are suspect since Hogan kicked out at 2 at the Shea show, and Monsoon intentionally fast counted Hogan at their MSG match.
If 1990 counts, then Rhodes wins easily. He probably did more jobs from Sep-Dec 1990 than in the entire 1980s.