To be fair, most of those e46 'deficiencies' you mention aren't present on the e36 equivalent.
I have a vested interest, I don't profess the following to be objective...
I think the e36 M3 deserves just as much credit, if not more, than the e46 equivalent, it was the e36 after all that heralded in 15+ years of ridiculously successful chassis and engine architecture. The e36 M3 was revolutionary, the e46 M3 was simply, and certainly beautifully, evolutionary.
The e36 M3 was the last truly analogue sports car BMW ever made, and a remarkable one at that, it deserves a top 5 position for sure.