Hey Andy - Lex has offered a reasonable alternative. I think it runs along the lines of - all the fuel you want and run-what-ya-brung!!! Ooops - plus multiple tyre compounds and/or tyre manufacturers.
I appreciate the endorsement, but I think you've taken numerous unrelated solutions/dreams and combined them into a single sensational formula
Overall, I think MotoGP has quite a few options to solve their problems. In another thread, IIRC, I said that MotoGP suffers from anti-competitive forces. As competitors fall out, the sport becomes less competitive, and growing consensus allows the manufacturers to create sterile competition. The governing body will never have the ability to split a dominant manufacturer into multiple teams, but they can create an environment that encourages competition.
Rather than trust-busting regulations, they could put restrictions on the winners. Everyone gets nine engines. If you win dry races, you get six. If you are the defending champ, 5 engines. Two-time champs, 4 engines. The purpose of winner's regulations is to provide steeply diminishing marginal returns just like anti-trust or anti-monopoly regulations. It could also spice up the entertainment b/c riders might leave teams after winning multiple championships which improves the competitive environment. Furthermore, the value of long dynasties increases as time goes on rather than decreasing as the manufacturers hoard and the fans get bored. The value of Doohan's 5-year run with a single manufacturer would have made him the GOAT along with Honda. Reducing fuel capacity could also be another form of anti-monopoly regulation.
In addition to creating unconventional anti-monopoly regulations, MotoGP could create an incubator to hatch additional fire-breathing dragons. By creating an 800cc Moto1 class with sensible regulations like 24L-800cc-specECU-16,000rpm, Dorna would have a place for FB Corse, Motocycsz, InMotec, Ilmor, etc to incubate. They'd also have a place for the independent chassis builders and riders to learn Bridgestone tires. If someone gets injured in MotoGP, replacement riders aren't hard to find. The exposure of Moto1 generates sponsorship revenues to fuel development so the smaller manufacturers can eventually create a MotoGP-worthy machine. Dorna could help the process along by paying companies to lease engines to other private teams.
An arrangement like the one I've outlined could allow MotoGP to have stable regulations for long periods of time. I can hear the manufacturers crying foul from here, but their complaints would merely reinforce my point about MotoGP suffering from anti-competitive forces.