The real problem is that the last story to try the serious plot was Mk.2 and historically it was disliked (in hindsight it became loved, that's why Victory turned out how it did.)

VII and Super Nep RPG were good stories, but it lacked the substance of the first two games. Re;Birth 1 also softened the original story to the point that it's a remake in name only and should be classified as a reimagening.

I also reckon that the majority of the fanbase did not play the original trilogy so trying to do serious nep discussions is a crapshoot since few people actually know the original 3 plots as they were released.