I'm well aware that Sailor V came about before the Sailor Moon franchise and thus we have a bit of retcon (perhaps a reboot?) of the Sailor V franchise in relation to Sailor Moon. That said,I honestly think that Naoko intended to go in a completely different direction with the Sailor Moon franchise initially, but that as the story evolved it became less feasible to return to that original story.

I get that Queen Serenity altered Luna's memories, but I still have a hard time grappling with her willingly allowing Luna to place the reincarnate Serenity in harm's way. She obviously knew that she'd reawaken to her identity as Princess Serenity at some point, but in the mean time she placed her reincarnate self in harm's way?

Sure Minako was acting as a decoy Princess, but what if one of the enemies decided to finish Usagi off before she awoke as Serenity? Of course this is fiction and thus we know that that wouldn't happen, but for argument's sake let's just assume that it were possible. Would the Silver Crystal necessarily manifest itself, or would it take her out?

I have to admit that we never quite get an explanation for her surviving her suicide, and Mamoru evading the blade via the agency of the Shitennou stones. I always found that to be just a bit too awkward and convenient storywise. Perhaps they were meant to die so as to see themselves once more in spirit form, to then sacrifice themselves so as to allow Usagi and Mamoru to live normal lives? I actually think that that would have been more romantic, and would have allowed more tension in the series as Usagi and Mamoru elected to be together on the basis of their own choice, and less because of living out their past lives anew.

I also think that it would have been better had the first Sailor Moon manga chapter focused on Sailor V's quest for the Moon princess, with Usagi being revealed towards the end. In short, have Minako occupy the position of Usagi throughout the series, and then later focus on the development of Usagi as Sailor Moon.

If I'm not mistaken, I do remember that Naoko intended for her story to only cover the first arc of the manga, and later on Toei pressured her to continue more arcs. Perhaps, this is why her story had a sort of "patchwork" feel. 

But even if that is the case, I do think she wanted to expand a bit on the lore of Sailor Moon, perhaps the origins of Sailor Soldiers, the nature of astrology and other esoteric elements in that universe, and how this all plays into the source of their powers.

That seems to be a more organic approach to the franchise. 

Infinity is my favourite arc (Black Moon, Dreams and StarS are my least favourites...), but that has to do more with the Outer Senshi being much stronger than the Inner Senshi, and there having the more distant relationship with Serenity/Usagi. In retrospect I do wish the senshi would have been allies as opposed to friends. It seems a bit cluttered/forced that they all randomly become friends.

This is my own speculation thread for an alternate Moon universe:

http://www.thegalaxycauldronforums.com/t12368-nehelenia-daughter-of-mamoru-and-usagi