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I have created a pull request [https://github.com/daylightstudio/FUEL-CMS/pull/609] that updates Fuel's jquery v1.7 with v3.7.1. It also updates CKEditor to the latest/last open source version v4.22. This is a major improvement and clears up a few Pen Test complaints and opens up fuel's custom fields support back up to new jquery plugins.
The repo for this is at https://github.com/croaker000/FUEL-CMS-JQUERY3
I'm happy to field questions bug fixes etc. there (or here) if needed.