That still doesn't justify using Pokemon at such high levels. Right now, the storyline seems most similar to the story in Ruby/Sapphire (not Emerald), where there is one evil team and their antithesis, and the former attempts to do something revolutionary while the latter tries to stop them. But Wallace's highest-level Pokemon is only Lv. 43. I admit that's a bit dull level-wise, and the rest of his team wasn't that hard, but since Milotic was a potential terror back in those days, it was still capable of being a difficult match (unless you used Kyogre, you cheaters!). As long as there's some kind of difficulty amongst the various Pokemon being used, you don't need their levels to be very high.
Maybe we can instate a sort of "policy" that if you use legendary Pokemon against gym leaders, they don't have to give you the badge.