Oh boy, villains, one of my favorite topics.

I slightly disagree on calling the bullies from LBT 3 "villains", mostly because they are kids, albeit older kids than the main five. They aren't not antagonistic, Hyp even threatens to physically hurt them, but he seems to do it mostly for that whole "I'm bigger and tougher and I'm going to keep and put you in your place because I'm the big boss around here and you better listen to me or else!" Granted bullies
can be villains, but I guess you as the writer or viewer will have to decide what exactly crosses the line from being just someone that is teasing to get a reaction to actually being a legitimate threat.
However, these other villains were definitely entertaining in their own right. Ozzy and Strut with how their dual personalities worked off one another, Ozzy being the egg obsessed brother that usually led and "hatched" most of the schemes to get the eggs and Strut the more docile, submissive brother that wanted to eat vegetation. I disagree with your view on Strut not being a villain MurMur. Just because someone displays more cowardly and vulnerable traits than another character who is more active, it doesn't make them less of a villain. Strut was the one that actually suggests they
kill Little Foot out of revenge taking back the egg they stole, to only have it hatch.
Ichy and Dil...they were more or less the same characters in nastiness and unpleasantness. One a blind and brutish prehistoric crocodile, the other a more slick and manipulative. But he seems to manipulate his comrade rather than anyone else. They seemed to just banter back and forth, picking at each other's flaws. They were sill predators to the main 5 plus Ali, don't get me wrong, but they were pretty much your typical sequel formula lackey type villains.
I remember holding by the idea that Pterano wasn't a villain or wasn't quite one to begin with, always having something of a heart of gold, almost like the Beast in BATB. Then I played a character in a RPG that was eerily similar to him as far as motives, his charm, and even had a bit of an antagonistic relationship to a kid he genuinely liked despite the fact that he used him as a pawn to further his plans for power. The character was Vlad Plasmius from Danny Phantom. Their story arc even ends with eerie similarities. While Vlad doesn't redeem himself while Pterano does, they are still both exiled and deal with the consequences of their actions.
Rinkus and Sierra, while they still do fall under that typical sequel lackey formula, I love that they inevitably turn on Pterano when Pterano can't deliver his blow-harded, fundamentally ill-lead promises of power. What's even better is when Pterano is in his "I'm awesome and everyone should love me" mode during his song, they PLOT against him, so even if Pterano succeeded in power they would still overthrow him, being power hungry flyers themselves. I'd love to see some mini series or something on how Pterano met these guys and what their relationships were like prior to re-entering the valley.
So ultimately? I choose Rinkus and Sierra.