Hi,
Yeah, I got a bit worried when I saw the title as well, it is considered rather distasteful and rude to discuss such matters as who takes over or what happens while Hatsumi Sensei is still very much with us. But I'm glad to see that the focus is on organisational matters here.
As to Menkyo Kaiden ranking in the various ryu-ha themselves, my knowledge and understanding matches that of Eric, but I would say that most likely Seno, Noguchi, and a few others most likely have Menkyo Kaiden in one or more systems, but can't swear to it. RVD has probably not recieved Menkyo Kaiden in particular lineages, in fact I think the mention of Menkyo Kaiden is a title he has conferred upon himself, deciding, as you put it, that because Jugodan is the highest "rank", then that is the same as Menkyo Kaiden. I haven't heard of anyone else claiming that their Jugodan ranking is Menkyo Kaiden...
A few years ago or so Arnaud Cousergue of France was awarded Menkyo Kaiden in Tachi Waza (specifically centering around use of sword, but having many other meanings as well), which is one of the only Menkyo Kaiden certificates I have heard of being awarded in relatively recent times. But this was a "created" Menkyo Kaiden in a specific skill set, created by Hatsumi Sensei to reward Arnaud for his dedication to understanding the use of Tachi, not a ryu itself.
Now to the question of whether or not Jugodan is the same as Menkyo Kaiden, well, no. They are different systems of ranking, and typically are not really related to each other. I see the Menkyo system as being related to the depth of your immersion in a particular specialised art (individual Ryu-ha, say, Shinden Fudo Ryu Jutaijutsu for instance), whereas the Kyu/Dan ranking system is based more on technical ability (at least in the early stages, up to early Dan ranks). As the Bujinkan doesn't really teach individual Ryu-ha as such, rather teaching a variety of skills and principles gleaned from the various sources that make up it's curriculum, then the Dan ranking system is far more appropriate. Remember, Menkyo Kaiden is far more than just knowing all the techniques, and being a member of a classical system is far more than just getting the movements. This teaching approach is the main reason the Bujinkan methodology is classed as a Gendai Budo rather than Koryu.
So, to answer your question in particular:
1) No, Menkyo Kaiden in the Bujinkan is not Menkyo Kaiden in the individual Ryu, that would be separate again, it would just be Menkyo Kaiden in the teaching methods of the Bujinkan. And as stated, I don't really know that the term Menkyo Kaiden really applies, regardless of what RVD has on his website, unless there is a separate certificate stating Menkyo Kaiden from Hatsumi Sensei.
2) As far as I know, Jugodan in the Bujinkan is Judan in the Bujinkan, at the highest awarded level, nothing to do with a Menkyo system of ranking. So no, Jugodan is not the same as Menkyo Kaiden in the Bujinkan, that would require separate ranking certificates and a separate ranking system.
3) There have been major exodus' from the Bujinkan before, and there will be more in the future. Different people have different values. As for what will, or may, happen, well that is unknown. It will depend on a number of things, including if Hatsumi Sensei even leaves a designated heir, and in all likelihood we may see a situation similar to Kyokushinkai after Oyama Sensei passed. There was a splintering into different organisations, each following the person they chose. This is not uncommon in martial arts, so I don't see much of a problem. But that's enough on that.
As for whether things are lost in the amalgamation of the various lineages, I would say yes, they are. But they are lost for a specific reason, to create a seamless collection of applied principles. The individual subtleties of the particular ryu may be missed, but they would typically go against the rest, so they are best left out. Think of things like the footwork of Gikan Ryu's postures, and how different they are to the rest of the Ryu-ha kamae to get what I mean by that.
But the Genbukan and Jinenkan doing better? By and large, the bulk of the training in these organisations are similar to the Bujinkan, taking from each of the various sources to develop and establish skill sets, and only looking to individual Ryu-ha after years of training (in the Genbukan's case, you only start training and studying a specific single Ryu after 3rd Dan). The Jinenkan trains each of their systems (Togakure Ryu, Shinden Fudo Ryu, Kukishin Ryu, Takagi Yoshin Ryu, Koto Ryu, Gyokko Ryu, and Jinen Ryu [Manaka Sensei's creation]) according to the scrolls, keeping the techniques in the exact methods and order as written. These methods are indeed better if what you are after is centered around the individual schools themselves, most likely from a historical/academic perspective. So it is up to the individual which is a better match for them, really. But both approaches (Bujinkan or Genbukan/Jinenkan) are right, just from different perspectives.