It also helps that there was at least a rough plan for the prequels, regardless of their eventual execution. Anakin’s fraught relationship with Obi-wan, the loss of his mother, the forbidden love…these storytelling decisions are in service to his character and in the hands of a better director they could have been realized brilliantly. On the other hand, the storytelling decisions of TROS act in opposition to Rey’s character and actively undermine it.
One caveat however - Anakin’s murder of the Tuskens does turn Anakin from sympathetically flawed to ‘bad apple’, but at least it’s not the cornerstone of the story like Rey Palpatine. That puts AOTC above TROS for me, if only slightly.