The following simple script reverts the most significant one of the inbox ‘improvements’: it marks all inbox messages as read as soon as the inbox is closed.
// ==UserScript==
// @name Stack Exchange: Automark as read
// @grant none
// @match https://*.stackexchange.com/*
// @match https://*.superuser.com/*
// @match https://*.stackoverflow.com/*
// @match https://*.mathoverflow.net/*
// @match https://*.serverfault.com/*
// @match https://*.askubuntu.com/*
// @match https://stackapps.com/*
// @exclude https://chat.stackexchange.com/*
// @exclude https://api.stackexchange.com/*
// @exclude https://data.stackexchange.com/*
// @exclude https://openid.stackexchange.com/*
// @exclude https://area51.stackexchange.com/*
// @exclude https://stackexchange.com/*
// @exclude https://contests.stackoverflow.com/*
// @exclude /^https?:\/\/winterbash\d{4,}\.stackexchange\.com\//
// ==/UserScript==
document.querySelector('.js-inbox-button').addEventListener('click', ev => {
const target = ev.target.closest('.js-inbox-button');
if (target.getAttribute('aria-expanded') === 'false')
return;
const markButton = document.querySelector('.js-mark-all-as-read');
if (markButton.disabled)
return;
markButton.click();
}, true);