Gary Motherfucking Oak literally tells you right before the fight he caught 40 Pokemons, therefore him just not using the full 6 Pokemon slots is probably so he has to focus on training less Pokemon (similar to how Ash had at some points just 5 Pokemon in his team and Krabby was with Oak).
His Raticate probably just fell of compared to other Pokemon and got replaced and the whole "one of his Pokemon died" thing could as well have been a different older one or sth.