As an outsider with limited information, I can only state my belief (regarding the root of the dispute over the direction of the company) that the Bolshoi benefited a lot from performing new works - creations, reconstructions or good stuff from outside. Ratmansky's Flames of Paris and the Bright Stream have become signature Bolshoi productions. To me, apart from their drama (on stage, I mean

), this openness to innovation is what sets them apart stylistically as a company from the Mariinsky (who built their identity around the preservation of classical traditions, but sometimes get criticised for stagnation). In the last decade they've stayed on that route (Taming of the Shrew, Nureyev etc.) and it definitely doesn't look to have hurt them in terms of classical technique. Striking a balance between new and old is a challenge most companies have to face, with some faring better than others (e.g Royal under Kevin O'Hare, though nobody's immune to detractors). Perhaps in Russia the involvement of politicians and businessmen escalates things...
Regarding Vaganova, thanks for the clarification about Dorofeeva. At least my perception of the opposition to Tsiskaridze at Vaganova is that it's not simply that they don't trust Moscovites, but they're afraid of losing the stylistic identity of the St Petersburg school (a style that some might consider antiquated). Although there are many Vaganova alumni among the teaching staff and artistic director so personally I don't think it's a huge concern... The only difference I noticed when I visited a few years ago was a weird class leotard colour scheme and a ban on Gaynors (sensible). I'm just not a fan of government directly interfering with school management. It would be great if he is universally welcomed, and if he put a stop to alleged embezzlement, although both of these points come from his own accounts. P.S. not sure what Filin was complaining about since Smirnova came to the Bolshoi in 2011...