I kind of resent Inafune's rejection of 3 and his rose-colored goggles that somehow give him the idea that 4 is regarded as superior.
I actually think he's pretty spot on. Megaman 3 didn't feel quite the same as the others. It also had some really lame segments, like the Doc Robot Needle Man stage. The mood was very different. It felt darker for some reason. This doesn't make it a BAD game, but it does feel like somewhat of a black sheep. For this reason, some people like it more, because it is different.
There were even portions where you could actually get the game to trap you with no way out, forcing a console reset. That does make it kinda bad in my opinion.
I however don't mind the addition of the slide. I think Inafune didn't like that much. He really seems to push the 'simple gameplay' idea. This is especially evident in Megaman 9. Inafune did seem to like the idea of the charge shot though, from what I've read out of Official Complete Works.
I do like 4 a lot more as well, and generally consider it to be superior. It feels more in line with the feeling of 1 and 2.