I know the last post on this thread was made nearly eleven months ago, but I have to say, this is a really cool idea for a meta! The change is pretty simple, and it doesn't really affect gameplay mechanics directly that much, but it drastically changes how one would go about playing because half the time you can't even be sure of what you're up against. One thing that might be worth noting is that it might be a good idea to avoid using abilities that announce their identities upon switch-in even if they're superior to other options that Pokémon has if you're aiming to trip up your opponent, as that will narrow down your Pokémon's identity further and often serve to give it away entirely. Also, lure moves in general will be more effective thanks to the disguise mechanic; simply put two moves that could conceivably be run by another Pokémon in your first and second slots, and use moves that hit that Pokémon's switch-ins effectively in your third and fourth. Not perfect, but probably the best way to go about it.
Also, I agree with the idea to have Mega Evolutions disguised as Sigilyph if that's possible to implement. Mostly because that's hilarious, though.
(don't have any set ideas right now, sorry)