Pythor and the Overlord probably should have come back to Ninjago sometime between season 3 and season 15. Because I legitimately think the chemistry between Scott McNeil and Michael Dobson was electric. Those two bounce off each other so well. I don't know if they'd worked together in the past, but I think I've seen some shared work on their wikipedia pages.
The Overlord feels like a villian they could've reused many times over, to be fair. He's basically a god. And although I haven't actually seen the finale of season 3 yet, I can't imagine any way you could ever kill a god. At the very least, it'd be nearly impossible. Where there is light, there is always shadow. The Overlord survives because he's basically a force of nature. He can't be killed. At best, I think you could imprison him in secretive and heavily guarded prison. Maybe trap him in an object, then bury it at the bottom of the darkest ocean or something. You can't get rid of him. You can only fight him in the endless cycle of light and shadow. Or something like that.
The Overlord is basically impossible to beat. Pythor is capable of being beaten, though. That one is fair to say. I think Pythor can be beaten, considering he barely clung to life after the great devourer ate him. So he's the easier villian to deal with. That being said, I still think he could've come back in cameoes during one of the seasons between 3 and 15. If season 3 ends with him arrested or something, really just play with him becoming the weird guy we see every time we have to have a jail scene or something. Perhaps he has knowledge the heroes need, so we have to have an interrogation scene. There's options, is what I'm saying.
Pythor could've made some fun guest appearances, I'm convinced of that. He basically stole every scene he was in, largely because of the voice actor's performance. Of all the serpentine we see on the show, I think he really embodies the negative use that Snake has as a term used for humans. When we call other humans snakes, we're usually calling them devious and cunning. We're calling them liers and manipulators. And really, I feel like Pythor is the only serpentine in seasons 1 through 3 who even remotely embodies that. Some others have tried, but none can match the constant duplicity of Pythor.
So yeah, I think these two made a good double act. They're both good on their own too, but I'm kind of amazed Ninjago didn't just to doing a Legion of Villians plotline sooner. I'm not going to complain too much, because I'm sure the villains for seasons 4 to whenever are probably all somewhat compelling. But I do kind of think they could've used these two a little bit more before the final season of the show. At the very least, I think they could've had them making cameoes in some of the later seasons to build up to their return in the final one.
I don't know too much about the later seasons, to be fair. Honestly, I don't even remember how season 3 ends. I have vague memories of seasons 1, 2, 4 and 5 from childhood. Maybe 6 too, I can't remember very well. But season 3 and seasons 7 to 15 are basically blank slates in my mind. So I'm basically engaging with the show as if I'm stuck in the past, kind of because I am. I don't know where things go, I mostly just know some vague details from lots of wikipedia reading.