I don't think there's enough from the films that might lead to this theory being seriously true, if anything I think it's almost like a joke from the part of the creators. Still, there are a number of coincidences that would make sense, and I think that's the funny part, such as Jar Jar's eyes having that yellow Sith color, being from the same planet as Darth Sidious and that he gave full powers to the Chancellor in Ep.III.
I love that the stop motion parody Robot Chicken Star Wars actually "confirms" this to be true (and actually, it might even provide an explaination on how could Palpatine have returned in Ep.IX).
Also, I watched the Clone Wars animated show last year and Dave Filoni remained in the same position, as in, you can't tell if Jar Jar is actually a Sith Overlord in disguise secretly moving on with his plans or just the goofiest character ever. For real, he nearly killed General Grievous by himself with a spear at one point while none of the Jedi masters ever managed to injure him!
By the way, I find the Clone Wars show to be best Star Wars content since Ep.III. I can't deny that I have a soft spot for the sequels and Rogue One, but I hate how Disney sabotaged each and every movie with their own hands and crashed the trilogy which had a lot of potential. Overall, the Clone Wars really adds a lot of depth to the SW universe, and while it has some flaws, its merits really overshadow the issues.