I don't think it's mutually exclusive to have favorites, have a favorite core team, and have specialist teams.
Snake-Eyes is one of my favorite fictional characters of *all time*, not just in context of ARAH. I have absolutely zero interest in a Joe team without him (or certain other characters, but mostly him). I have less than zero interest in anyone else cosplaying Snake-Eyes in-universe. I feel the same about Cobra Commander and much of the Cobra top brass. The characters are the point.
I think you just nailed the very niche age difference thing with the Joes line specifically. Cos Neon Green v1 Sci-Fi is an all-time favorite. The Low-Light we have now - perfect to me. OG Stalker absolute fave (though admittedly OG was lost and so tundra Stalker took over as a fave for a long long time... I'm dying to get puffer coat Stalker soon.) Spearhead is our overlap, probably because of his release year.
I'm just the right age that the cartoon vs. the file card baffled me. "Why doesn't he talk when the guy I have at home loves talking to everyone?" THe Thomas Magnum thing is why I love him. He'll always be a favorite. I didn't hate the cartoon version but that was just some other guy in a Hawaiian shirt.
I played VERY weird. I was in an arts program in elementary school that was supposed to be I guess gifted and talented adjacent and one of the projects they had us working on was building an underwater city. I ended up using either MASK or Joes to inhabit the city, everyone had a story, and the teacher looks me dead in the eyes with an expression I'll never forget and said "You'd do this at home all by yourself, wouldn't you." This kid was always off with the faeries so to speak.
I feel kinda the same, but I did really enjoy the IDW stuff with cult leader Serpentor, creepy Crystal Ball, and CC getting killed by Chuckles then the high command making a contest for who would take over the position. In an elseworlds kinda way. Which I guess is how I see the comic versus the cartoon anyway.
It’s one of the things I love most about the comics. Hawk rules, Duke drools.
I dug that story too, but the Cobra Commander “rotation” elements keep it from being a favorite. I totally get why they did it and it is absolutely a cool swerve, but it’s like in that shitty Dracula 2000 movie when they’re like “suprise Dracula is actually Judas Iscariot” and I just had to nope because they literally tossed out the original character I love so I no longer care about that story.
For some reason, I don't hate any of the Cobra Commander weird revisionist history backstories, to the point where I look at him like the Joes universe Loki. How is this gaslighting madman screwing up our world THIS time? Meanwhile in every universe to me Snake Eyes is the same. It's like they're the yin and yang of my Joes head canon/collecting habits. Every weird ass Cobra Commander story is valid. But Snake Eyes always burns his face in a helicopter crash, loves Scarlett, and learns to Ninja from Storm Shadow's family. He's an anchor being, Cobra Commander is a chaos factor.
I mourned TWICE for Prime: once after the movie, and then I had a fucking MELTDOWN when he came back but was essentially a Quintesson-controlled zombie and sacrificed himself (they showed half his face get blown off!! Holy shit!!!!). I put up a memorial in my closet. I celebrated for WEEKS when he truly came back during the hate-plague and kicked Rodimus’ infected ass and they played YOU GOT THE TOUCH!!