The control tire must die.
Keep a standardized compound (or set of compounds) if you like, but allow/mandate a wide variety of carcass characteristics, including custom builds. (But no overnight specials for the Yellow Clown or Golden Boi.)
IMO, this will do more to get more riders up to speed than any other single change. (Remember some dude named Elias?)
Got chatter? Rather than spend untold millions on swing-arm, chassis, and shock mods, just drop in a different tire. Even w/o chatter, a variety of tires will greatly simplify chassis development. If Ezzy really wants the CRT crapwagons to compete, give them tires they can use out-of -the-box.
Beyond that...
Bird's turbo suggestion sounds fun, but 600cc will be WAY too much. The 1500cc F1 grenades made 1500++ HP at god-knows how many PSI of boost (probably around 90). As much as I'd like to see one, a 700HP MotoGP bike is not remotely practical. Will need to limit the pressure ratio. 500cc at 4 bar and 12000RPM is about 300HP
Free engine configuration. This might invite other manufacturers to enter the the circus. Allow Triumph to run a 3 cylinder if they like. Or a Guzzi twin (with another few cc or PSI of boost, perhaps.)
Screw fuel capacity limits or delivery rates.
Every Monday following or Thursday preceding a race is a free test day. No or very limited fly-away testing during mid-season. More value for the fans and lowered expenses for the teams.
Limit electronics to basic moon-shot protection. No corner-by-corner torque mapping, no anti-wheelie, etc. The programmers can amuse themselves writing code to optimize the turbo's power characteristics.
Oh yea, fire that ....... ..... Ezzy!