Erik is right that the new checkboxes look weird next to the old style controls, such as on Preferences. Since we don't want to add new controls that teams don't yet need, why don't we just remove the checkboxes for now, and just focus on getting text input + button styles out the door?
I'm fine with this. If we want to do this we should setup a tracking bug to make mw-ui-input the default and attach all the relevant bugs. We can use the $wgUseMediaWikiUIEverywhere global for checkboxes, and then later select and radio buttons.
Reducing scope anywhere we can is great. I'm confident that once these controls become more visible in more places we will see development on MediaWiki UI speed up. .