Nice thread, interesting theory, and well composed.
Kabuto said to Edo Madara that Tobi doesn't seem to be following the original plan via Muu's voice, but that Kabuto is here to work for him (or something along those lines). To me this indicates that the original plan was conceived at least in part by the original Madara and perhaps Izuna since for a while they did everything together, but I don't when it was conceived.
Madara grew up in a time of war from baby to his fight with Hashirama basically because he could not accept the peace with Hashirama and the Leaf. Further, as the one of the strongest, if not the strongest descendants of the elder son, Madara shares his view with peace by force (e.g. Infinite Tsukiyomi) as opposed to love, which the younger son proposed. I think Madara handed this task off to Tobi when he knew he was going to die with the agreement that he would run things until Madara returned via Rinne Tensei not Edo Tensei. All these things point to this all least being conceived of by Madara and Tobi is using a variant of it to suit his personal needs as well, which we learned more about in the last chapter.
After all, Tobi knows the suffering of being "No one," and the quickest way to change that is to make himself someone by being supra-human as the Juubi Jinchuuriki (Tobi stated that this made the So6P's supra-human at the Kage summit). Further, look at what controlling their Bijou has done for Naruto and Bee who were already excellent shinobi. Then the world won't have to sit up and acknowledge him and his plans because they think he's Madara but because of
Tobi's own power.
I think that Tobi can still fulfill the Infinite Tsukiyomi going this, his current, Moon's Eye plan route, but with recognition and awe of the ninja world in the process, for who he is and without Madara's name. Further, he'll have power to stand up to Edo Madara if needed, as he'll no longer have a body that will be a shell of its former self. Something I'm sure Kabuto and Edo Madara don't want given Kabuto betrayed Tobi and Edo Madara already has his hands full. I suppose Kabuto does too with Itachi (i.e. Edo Chuck Norris) coming after him, and god only knows what Sasuke's doing, possibly might run into Kabuto, though I don't think Kishi would make a big thing of it, and given he's
currently insane "in the darkness", we won't get to see the great duo of Sasuke and Itachi, which is disappointing.
Edit: A couple of points, to address yours at the bottom of your post.
1.) I recall that when Yamato was captured that Onooki's number one fear was the extraction of knowledge by Madara's doujutsu, which he regarded as extremely powerful. Given that when he was very young when he saw Madara, Onooki may have been over frightened but I think the panel showed him to be old enough to have reasonable judgement and now tempered by experience to be fearful of Madara's genjutsu even though he's been using ninjutsu, which is most appropriate here for large scale attacks. He's taking out both major players and cannon fodder. It's impractical to try to Tsukiyomi or whatever his MS genjutsu is on all of them. Further, if I recall he did catch one in genjutsu during the fight so far.
2.) Shisui's eye would not work for Infinite Tsukiyomi, first for the obvious reason, namely that it doesn't cast Tsukiyomi but his MS genjutsu was Kotoamatsukami, so I guess at best it would be like eternal Kotoamatsukami, but his genjutsu appears to already be permanent unless it's discovered or something. Itachi's hasn't been broken for example, but the one on the Iron country Samurai has. The problem with Shisui's is that his genjutsu just gives you ideas or commands that you think are your own, while Tsukiyomi creates a new reality for the user that reshapes their entire space and time (Itachi could stretch it to at least 72 hours, this would be eternal; thus, a lifetime practically speaking) at the control of the genjutsu caster, and that's what Tobi & Madara want everyone to be in while they manipulate space to generate peace by force, which is the way of the elder son.
Peace