I'm in the same boat, except that most everything runs fine but Chrome is pretty much unusable. I'm wondering if a factory reset would help or not. Any thoughts?
(OP: I don't mean to hijack your thread, I just thought you might be interested in the answers, too.)
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Amazingly, I did a few things that helped speed up my Nexus 7. Funny how it worked because I have been experiencing this problem since the latest update.. I literally couldn't load apps for at least 2 minutes or so...what a waste of time! Last night I spent a couple of hours doing the following:
Removed unnecessary apps or at least reinstalled the ones I need, including Facebook.
Dragged each heavy file app to App Info and cleared cache. Chrome and Google + had the most amount. I did plenty of cache clearing until I'm satisfied.
Stopped most of the cached processes in the Apps in the Settings
Uninstalled the latest updates on internal apps like Youtube and IMAP, which restored it to factory settings without deleting data.
After doing all this, my Nexus 7 went back to normal loading speed! Note that I neither did a complete factory setting reset or regression to KitKat. Hope this helps.