Other than the ability to uninstall it with native tools there is no difference that you, the user, can see. Just as a fair warning: if you uninstall a system app, it will not be installed in a factory reset. You will have to flash the stock images to get them back to system apps. Titanium backup may be able to 'convert' the apps for you but I can't remember. Maybe someone else does?
I personally have moved all Play apps other than the Play Store to user apps. It makes it easier to install updates before the rollout hits me. Plus if it decides to misbehave I can quickly uninstall and reinstall. And I can uninstall what I don't need and a factory reset doesn't mean I have to hunt through them again to remove.
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