1- We don't really need barrett and aero or at least not use them in the exact way the development team was going to. really they didn't seem to reveal anything about megaman or the actual storyline so don't limit your focus to what they were working on.
2- Main villains. If this game is a continuation of the original storyline we need new villains and a reason for their existance. The mothers have both gone over to megamans side so all thats left are reaverbots and likely other units like Juno. I think that the bosses for MML3 should be made up of other purifier units. Remember that megaman is simply a first class purifier unit. What about second or third class units? And what about a leader or even other first class purifiers? There were 2 mothers there have to be more purifiers, maybe ones that activate now that megaman and both mothers are malfunctioning.
3- We need to be thinking about a conclusion. I like the idea of having megaman travelling to islands and protecting them from reaverbot attacks. The reaverbots I assume have become active as part of the carbon reinitialization program so we can have them at times leave the ruins and come out on the surface.
Do we want connected dungeons like MML1?
How many extra ruins can we add for exploration?
How will megaman lose all of his weapons this time?
There are a lot of questions to answer, maybe we should make a list of questions and possible answers, then create an overall outline for the plot and fill in the details as we go along. Any thoughts?