Feel free to edit or delete as it is not a cure for everyone and we don't want to confuse people.
However, after the patch for 5.0.0 there were tons of issues logging in, launcher not recognizing my server, having to use work arounds, heavy lag and disconnects in raids, many of the reports on this entire forum were mine, with exception of hardware issues. However, in order to be assisted, there was always a request for hardware specs, and then work arounds given. Even though I didn't have the hardware issues, I used the work arounds which as I recall always involved deleting/trashing certain files and relaunching. I either saw improvement, or no beneficial affect.
Sadly, game play was still not acceptable after 3-4 weeks of this. I finally broke down and did every part of https://us.battle.net/support/en/article/uninstall-reinstall-instructions-for-patching-issues
with the exceptions of deleting the battle.net files, add on files and log files, only because those weren't specifically asked to be deleted. However, to restate, "the work arounds involved deleting/trashing certain files.." and the uninstall process pretty much deletes/trashes them all.
Results: Very good fps increase during low fps fights. Make sure to launch the 64 bit client, when I did the first one, I actually had latency I hadn't seen yet, switched to the 64 bit, and normal latency. My character bodies and spell bars shows up after the load screen immediately, rather than the 25-30 seconds it took every day but today. And the fps issue is severely improved in fights that there were problems listed above. It isn't quite good enough, and still frustrating, but it is good enough to be useful to your raid or bg teams, as they probably won't notice the difference now.
Possibly Machkhan, as you suspect, there is something in the old data files that isn't playing nicely with the new programming, and maybe it's just better to remove all the old stuff, and let the new downloads play nice together.