Jinn assumed Maul was a Sith because of his Sith tattoos. However not that they changed his backstory to Maul having his tattoos since birth, it makes no sense. Qui-Gon encounters a random Dark Jedi and just assumes it a Sith?? The fact that he just discovered the Chosen One lends some credence to his claim, but still.
Source? Early EU sources say they are "Sith tattoos" but not that Qui-Gon recognized them as such, as far as I know.
If you've been in hiding from the Jedi for 1000 years- it doesn't really make sense to have something spelling out your affiliation tattooed on your face. I'm ok with the "They're Dathomiri tattoos" retcon. Especially since Qui-Gon doesn't give a reason why he thinks Maul is a Sith Lord. If he'd said "I recognized the man's tattoos from history books about the Sith" it would have been different.
I never got the impression, long before the PT came along, that Palpatine was unfamiliar with a saber, or even "awkward" in his handling of it. Reading this thread is actually the first time in my life I've ever heard of anybody having an issue with that. Thought has never crossed my mind. And what's interesting about this discussion to me is that I was one of those kids who spent time dreaming about Palpatine and Yoda wielding lightsabers. It never once crossed my mind that they didn't in their younger days. I always assumed they both were capable, but didn't face any real need to use one at that stage in their advanced lives. I saw "old" Obi Wan and Darth Vader using them, so it just seemed perfectly logical to me that the Emperor and Yoda could use them likewise.My dream Star Wars match up? It was Yoda vs Palpatine, with lightsabers. I kid you not.