Browsers automatically attach cookies to HTTP requests, opening the door to attacks like CSRF.
The security impact of automatic client-side expiry is tiny, since token expiration must be done server-side anyway.
The HttpOnly flag as an XSS mitigation is almost useless; competent attackers will simply run their code from the victim's browser and session. To protect against XSS, HttpOnly doesn't really help you at all. You should be setting a CSP that prevents inline and 3rd party scripts by default, and whitelist what you must.
Overall, cookies may seem like they have a lot of security features, but in reality they are just patches over poor original design. IMHO, using local storage is probably better, because there's less room to get it wrong.