Right now jQuery3 may break some things in our controls. R2 2017 SP1 will be the first release to bring workarounds. After that other workarounds may get implemented, depending on what gets reported and its severity.
On the size - the MS AJAX library alone is almost 500kb in debug mode, and 150kb in Release mode. Add a simple script manager to a page and monitor the network traffic.
This does not take into account the other scripts and stylesheets on the page which often amount to several MB. So, the 90kb of the embedded jQuery are not likely to be the biggest hit on performance. If you enable the various CDNs, such resources will get cached and speed will improve greatly.
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