Ariados and Espeon attacked Latios and Latias when both were fleeing. Obviously, the strangers and being pursued would've confused them; they're used to seeing Bianca and Lorenzo. Neither Latias or Latios have tried to fight back, as far as I can remember, and when under attack, they tried to hide themselves with cloaking, which Anne and Oakley did detect with their.. heat vision glasses..
And when Latios attacked Pikachu, Pikachu was unaware of the force against it. Latios was under cloaking.
I don't think the legendary Pok?mon that were "priased so highly" got "weaker" as the movie progressed. If you've noticed, a majority of them had been captured unexpectedly with devices that specifically honed their powers. (i.e. Articuno, Moltres, and Zapdos were caught by some weird ring contraption, as did Latios.) If you've been imprisoned inside a cage that zapped you whenever you tried to move, I think you'd get weaker, too.
And.. Yeah. I agree with Dark Weezing's second bit. The more playful ledgendaries don't seem too keen on using their powers and are quite immature. They most likely won't try to fight back.