If you are set up for a new development and are not really dependent on any of them, you should definitely go with QJSEngine. There are a number of articles that you can find explaining the difference from a technical point of view, for example
I would suggest looking at thread also this one.
Currently, QtScript is a purely compatible part of Qt, does not have QML integration, and has not been updated / supported for quite some time in favor of the new engine.
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