One of the polls I showed had MM6 well above MM7, so I don't see your point.
I strongly disagree with that. MM7 had choices and branching paths. The idea of the scavenger hunt, rebuilding a castle, and being caught in the middle of a war and deciding the outcome are novel concepts. MM6 had a more traditional story for its time.
You're not taking into account how popular Heroes of Might and Magic was at the time. This was at the height of Heroes popularity. A story that ties both M&M universes together was pure gold for most players.
Coming from someone who has played every M&M game and Heroes game that is my theory on why M&M6 is remembered more fondly. Plus you got an awesome shirt when you bought M&M6. I still have mine Not to mention Larry Elmore did the art on the M&M6 box. You are talking to a M&M historian so if you have any other questions that need to be answered ask away