Board Thread:Manga/@comment-36363526-20180728083423/@comment-26495049-20180729163246

Jean has a beard, though. This guy doesn't. That's the biggest difference for me.

Besides, there wouldn't be any emotional implications for Jean being the father, as Jean hardly ever (has he ever?) talked to Historia directly or has any past history with her.

Looking at it out-of-universe, it wouldn't make for an earth-shattering revelation if Jean were the father, which means Isayama is unlikely to go that path.