Personally, I favor there being no "powerful" subraces at all. Since you're making your own sure race system, rebalance and redesign all of the races to be in line with what you want. I personally recommend adopting 5e.
Dwarves get +2 con.
Hill dwarves get toughness for free.
Gold dwarves get +2 strength.
So on, all races have representation in the books. And since you'd be updating to 5e races, technically all dwarves would get +2 Cha from to remove the 3rd edition negative trait, making it a flat stat like humans.
Anyway, point being, by adopting 5e races you are also balancing drow and duergar and removing their "powerfulness". Do this for all of these races, and just never, ever include powerful ones like half-dragons and lycanthropes.
If the DM team feels they want a half dragon villain, they shouldn't do applications, they should agree on a player and offer it. Same for lycanthropes. Don't allow requested on creation werewolves, instead make a plot about werewolves and offer one or two players on creation wolves (whomever is around, available, is trusted with the power, expected to be cool, and hadn't recently been honored similarly) and let them infect players.
Alternatively, I'd simply make it require 3 DMs to sign off on, with veto power on creation if it doesn't work, or if the player abuses it. Maybe don't make it an app, just a lobbying thing. Player must get sponsorship from X number of DMs. That's for blanket applications though, not just subraces. Obviously the more powerful the app, or more weird or prestigious, the fewer DMs will sponsor it, so you elininate the silly confirmation periods and slow voting process. Just present your idea to DMs until you get the appropriate number necessary to app.
Generally though, prestige classes and earn in game things should really be obvious and easily obtained if actually earned.