OK so Youmu has a couple options here.
Let it pass: we could apologize to the Zapdos for interrupting it, and go on our way. We don't get any immediate benefit from this encounter, but it might show up later or influence later events.
Pokemon battle: we could bring out our pokemon to fight the Zapdos. Our pokemon aren't very strong yet, and the weather and terrain aren't to our advantage, and the Zapdos could choose to fly away.
Challenge it ourselves: we could try to fight or intimidate the Zapdos by ourselves. This would go against Reisen's advice, but if the Zapdos is trying to see if we're strong or not, we should oblige it like a good samurai
Nonviolent recruitment: we could try to get the Zapdos the same way we did Sora and Opal. If we decided to do this, we'd have a further choice as to how we'd convince it.
>The Zapdos is immense, but how big is that? Is it as big as a horse?