Oooh do you mean the color of the soccer ball? I always wondered how that's determined. Maybe related to Rilan's point about species.I've found that it's based on EVs. Are you sure they had the same soccer ball style shot thing? (No idea what you'd call it) My guess is they both shoot different soccer balls which score differently...
Yeah you're probably right. According to online guides, attack / sp attack = higher scores, defense / sp defense = faster shield recharge, speed = shot and movement, and hp = fewer points lost if soccer balls hit you. I haven't seen a totally comprehensive guide though.I think it's based on the Pokémon you pick. They're kind of like the Pokeathlon stats, each species shares the same statpool. I have a handful of Volcaronas; some flawless, some far from. In the end, after EV training, they seem to score similarly, almost 2k points for each charged shot(green). Yeah, EVs do influence how you score. They scale higher as you gather more, being more effective if you aim for Attack/Sp. Attack. Same goes for how Speed influences shot and movement speed. The Defenses I believe just weaken shots against you, I haven't been hit much though.
I actually don't think legendaries are necessarily better at this. Talonflame outscores Mewtwo, for one, and none of my pokemon ever hit above even 500 points. The secret levels were pretty hard and took me a while to clear. My strategy is just to hit (without charging) as often as possible to hit the point threshold before the balloon bots / soccer balls drain too many points.