Often people use an incorrectly sized logo for $wgLogo. We should consider adding to skin CSS something like .mw-wiki-logo {background-size: contain} .mw-wiki-logo {background-size: 135px} in order that the logo be scaled appropriately.
Downside, is users might not see brokeness, and then not fix their logo size, which is the ideal outcome, as too big a logo is bad for bandwidth.