As of Asset CleanUp v126.96.36.199, a new option is added to the plugin’s “Settings” page which is meant to help you switch from the Enhanced “CSS3 iPhone style checkboxes” to the Standard (basic HTML checkboxes). Switching it from “Enhanced” to “Standard” is useful if you use a screen reading software (e.g. for people with disabilities) and you’d like to have full support by falling back to clean (without any CSS3 code) HTML code. It’s also up to people’s preferences. Some like the iPhone style, while others prefer the old standard format.
To change this option (for checkboxes inside the settings page too), go to the “Settings” page, change the radio button from “Input Fields Style” and click the “Update” button. On page reload, it will show you the new updated style.