Doctor Walter Bishop said:
never team up with my friend at the battle maison
he's a dick and his krookodile keeps using earthquake even though he knows you're a poison type
Having to work with a CPU partner can always be a big pain, since your ally could end up going after the same Pokemon as you, and has the tendency to use attacks, regardless of its teammates pros and cons.
Doing a double battle alone is much easier, since you can design your battle plan better; for example, have a Flying-type Pokemon be alongside an Earthquake user so that ONLY the opposing Pokemon would be damaged. Similarly, Telepathy can protect your Pokemon from its own teammate's assaults.