Dumbledore's motive is almost certainly stronger than Amelia's.

Which is why I think it a significant possibility that Dumbledore helped in some way.

Any of those defenses might be sufficient for a single clue, but you have to take the clues together. Three successive clues (plus her character) pointing to Amelia, and only some words spoken to Lucius that we never saw pointing to Albus (and everything else we know of his character pointing away from him, though I know some would argue that), increase the probability of Amelia's guilt quite a bit more than linearly.