I think the Classic mode for these two is actually more clever than it looks at first glance: the first opponents are the ones who started the power/speed team template (Zelda & Sheik), almost all of the series used were part of Pyra and Mythra's trailer, and Ryu & Ken also were used as a dichtomy in the presentation. Beyond that I found it nice that the items, when present, were themed after the series as well, in addition to the Street Fighter battle being a stamina one. It was like Pyra & Mythra were actually travelling to these different worlds.
When you can switch to being fast whenever you darn well please, would it even really matter if Pyra was even slower than Ganondorf? Chasing people is not what Pyra is meant to do anyway. You switch to her when you want people to come to you, or at least create an opening. Because even with all her speed and fast moves, if the opponent is dead-set on defense, it can be surprisingly hard for Mythra to dislodge them.