User blog comment:Pandawarrior/Mutiny on the Bounty/@comment-5869646-20151204151745

Remember how Kid's bounty was higher than Luffy's because he attacked so many innocent civilians? I think it's same thing with Jack, just on a much bigger scale.

We're talking about a guy who just went a destroyed an entire country because they didn't bring him the samurai he was looking for. They didn't even know about the samurai and offered several times to let Jack and co. search for him in peace, but Jack is so insanely stubborn that he never agrees to discuss anything or compromise, and "loves destruction". It's not hard to imagine him wrecking countries rather regularly, and adding to that he's one of the top crewmembers of a Yonko, so his bounty doesn't seem that strange.

Also, regarding Ace: He wasn't the 3rd in command. The divisions aren't ranked, all the division commanders are essentially equal. He only got the 2nd division because it happened to be without a commander. We also don't know when the Marines found out about his heritage (Sengoku was unaware of him at least back when he got his first bounty) and Ace certainly wouldn't harm civilians or cause much destruction.