I believe there are two at least of each. We know Brandon owned Regirock so let's assume he has Regice and Registeel as well. There's one of each, then the 'Rock, 'Ice and 'Steel that appeared in the Lucario movie. At least two of each species.
Originally Posted by burrut13
And I believe more strongly than ever that the Pidgey, Hoothoot and Salamence were Brandon's. My reasoning is simple: Noland owned all the Pokémon at the Battle Factory, same for Lucy at the Battle Pike. Brandon owns the Pidgey, Hoothoot and Salamence, he just allows them to live in the Pyramid outside of their Poké Balls.
All projects cancelled. Goodbye.