Protean is a darn broken ability, like Gale Wings.
I think Nintendo Game Freak had intended for hidden abilities in Gen VI to be much, much, much, much, much rarer.
I'm not certain on that. If anything, they seemed to intend to make hidden abilities much more common. In Gen5, the only way to get them in-game was grotto Pokemon, and that was B2/W2 only, recharged at a 5% chance every 256 steps taken, only had a 20% chance of Pokemon, and were limited to a tiny subset. Breeding them was female-only, and Ditto-breeding automatically nullified any chance of passing them on. Otherwise, you had to go online to Dream World. In Gen6, you get both Friend Safaris and Horde Battles, both of which are easier for the player to access and which, combined, give access to far more Pokemon in-game. Breeding also now allows males, as long as you breed with a Ditto. All in all, it's much more accessible than it used to be, and in a very systematic way; it's not the sort of thing that would have been tacked on at the end.
Genuinely, I think they just wanted to break some old trends (mediocre starters, terrible Route-1 birds/rodents) and went a bit too far in that respect. They've been doing that off and on; Staraptor is all sorts of smashy fun, while Blaziken, Infernape, and Swampert all were quite acceptable, and Chesnaught's biggest weakness is simply it has to share the same metagame with Talonflame. They definitely did a better job with Diggersby, though; Huge Power gives it quite an offensive kick, but doesn't cause it to overpower to quite the same degree as free priority or perma-STAB.