The speed boost was probably necessary, because there's another hoard of shadows coming their way. They're easy enough to defeat, but it's just the sheer number of them that's sort of wearing him out. Mako from his other life is used to fighting, and it shows in how he moves, too--dodging and swinging with ease--but the current Mako's body isn't as conditioned to do these sorts of things.

"Probably a good idea to start using it more, because they're coming now!"

A group of shadows rushes towards them at their left. "Your ten o'clock, John! Use your Persona!"