The series was never about Hamon vs Hamon though. It was Hamon vs Vampires and then Hamon vs Stone Men. The most interesting applications of Stands all seem to be with antagonists. So, really, they easily could have just continued the series with Hamon vs Stands.
Hamon was shown to work just fine against normal humans in Part 2. Knocking them out, controlling them, curing them, destroying things inside them, etc. It was specifically good against Vampires, but it wasn't really an ideal tool against the Stone Men at all. Joseph had to go way beyond the previous applications of Hamon in order to make it useful against the Stone Men. The first time he attempted to use the sunlight overdrive, it was completely ineffective, aside from barely keeping him from being absorbed.