Pocket Monster Reburst

The protagonists are Ryouga, a boy with superhuman strength, and Miruto, a girl who works for an organization tracking the villains. The plot centers around "Burst", the ability to use crystals with Pokémon stored in them to transform into human-Pokémon hybrids. Ryouga's Burst is Zekrom, and one of the villains' is Excadrill.
On rare occasions they actually use Pokémon.