Even if ignoring non-Game Freak tiers (which I'll do from now on), they realized it was weaker than the others. In fact, I would even say that Kyurem was originally designed to be weaker. Otherwise, I don't think they would have given it two new formes with 40 extra base total plus some new attacks with no in-battle drawback, given that it was already a box legendary, and already just as ban-worthy as Pokémon like Mewtwo or Arceus, according to Game Freak themselves.
They could have made Kyurem's formes' stats be redistributions of the original Kyurem's, like they did with Giratina, who was already on par with its fellow mascots. But they didn't, because they knew that it was weaker than its counterparts, and knew that it needed higher stats to be closer to them. Of course, Kyurem's alternate formes ended up having higher stats than its counterparts, but they also got a restriction of one per game, and require giving up one of the legendary dragons for as long as one wants to use the alternate Kyurem forme.
Primal Groudon and Primal Kyogre's restriction could be a one-per-battle limit shared with Mega Evolution, if their transformation happens in battle (which is what I think will happen). The alternative could be a reduction in their other stats, which would probably mean a redistribution like Giratina's in a transformation outside of battle.
Maybe all starters will get signature moves from now on, like the Kalos ones did.