Since you have taken the time to write this well constructed reflection, I'll take the time to respond. I have to say that I do very much agree with a lot of what you are saying; version 3.0 felt like a much more complete game whilst version 4.0b felt very much more experimental but stable. I remember back when version 5.0 was leaked - I never did download it (at the time I believe I did so out of respect for the creators) but I have seen videos and it does look very fun. It certainly has build upon the momentum which version 4.0b created and looks very promising. I think it is incredibly interesting to see how Megamix has evolved over time and in my opinion, the transition between version 3.0 and 4.0b is where the game started to feel less like a Sonic hack and more like an entirely new game itself. I am incredibly interested to see what the future holds for this hack in regards to design choices, implementations and how much the team can really push the technical limitations of the Genesis / Mega CD.
It was pretty obvious what the fate of this game was gonna be once it was confirmed there would be no Big the Cat fishing minigame.