If my memory serves me correctly, currently if you pre-render a map, and one or more of the tiles in that map are animated, then the animation simply doesn't work, because the pre-rendering takes precedence.

It would be cool if the pre-rendering still took place, but the engine also noticed that some tiles were animated, and honors that. Obviously it would be more draws, but I'm betting this "hybrid" between pre-rendered could still offer a big boost to performance.

Edit:

A bonus suggestion: Multiple occurrences of the same animated tile within any given chunk, could be "pre-rendered" into a larger animation that could be drawn just once. Basically just applying the chunking-pre-rendering algorithm on groups of animations that are the same.