On the Clear Body issue, I always saw it having to do with them being machine-like Pokemon. The Regis are sort of like ancient robots in a way, being animated rock, ice, and steel, and acting like computers in the movie. The way I interpret Clear Body is that machines are always working at almost perfect efficiency and it is very hard to slow them down, especially with the methods used in most stat reducing moves. I have no doubt this was probably influenced by the countless number of times I've seen Intimidate not work on Clear Body Pokemon. Machines can't be stopped by scaring them, or howling at them, or throwing sand at them, or saying nasty things to them with Parting Shot, etc. Yeah, these machines are still living Pokemon that do have emotions (maybe with the exception of the regis), but Clear Body is just a design reference to their machine nature.
Tentacruel and Diancie/Carbink are the ones that don't fit this. These two kind of fit the more literal idea of clear body when you look at them (semi-translucent orbs and diamonds). Although when I scroll back up, it looks like these are the two that Detective Barricade actually came up with an explanation for, which I think fits, so I guess we can just accept that there are two meanings to the name.
The more I think about it though, Clear Body seems like it would make more sense if it prevented the Pokemon from getting poisoned. But most of the Pokemon with it are immune to Poison anyway so it'd be a waste.
As for this new mysterious Pokemon, I've heard it interpreted as some sort of Zygarde larva which would make sense. It'd have to be a form though, not a previous evolution (or it could be a separate but related Pokemon, like Phione and Manaphy) and if it is a form, I really like Drake Balleydier's idea of it being an inverse Pokemon. The fact that it does not look like a threat at all fits the whole inverse theme too. Reminds me a lot of Lucemon from Digimon Frontier actually, a dragon who also has a larva form, as well as a form of a tiny unimposing child angel that is actually extremely powerful.