Merge two folders with conflict resolution strategy

When I merge two folders with rsync, if files of the same name exist in the "target" directory, those will be kept unconditionally. I can use unison which is a bit more advanced, but as far as I know it only looks at file creation time and picks the newer one. In my case, files under the same path with the same name are indeed semantically the same, but they might have different sizes. I want to merge based on file size and not creation time. Is there a utility that supports this case or do I have to write a script for that? Unfortunately, I can't give an estimate of how many differently-sized files will be encountered. Might be anywhere between a small double-digit number to somewhere in the 10'000s.