Until you see the last episode, I guess there will still be some things you don't know, so SPOILERS ahead. Don't read 'em if you don't want to know what happens. The last episode does sum up a good bit of the ongoing plot lines (though not all of them). We got good closure for this season with so much left to be done.
SPOILERS BELOW --
I agree with you about learning more about Mongo's history. They are now officially 'trapped' on Mongo (Flash, Dale, and Zarkov). Gordon Senior is back home with Flash's mom. Since their son is now trapped on Mongo (a reversal of the initial situation), I am presuming that Gordon will try to rebuild a rift generator on Earth. And possibly Zarkov will work on rebuilding one on Mongo since he'd have more funding and support there.
Civil war is inevitable. Terek may play out to be an evil character, and I'm fairly sure that when push comes to show, Terek and Aura will eventually end up vying for power, particularly if Terek doesn't turn out to be as compassionate a ruler as the people hope, and this may be the case given his lineage.
Plus, the other tribes/cantons are inherently antagonistic toward each other. As you've said, different factions will cause additional civil unrest eventually, inspite of a new ruler.
Also Ming's army is larger than Terek's united forces (Revolution part 1), and it's strongly implied that he escaped his execution and is w/ Azura. Obviously, he'll want to reclaim his 'throne' at the earliest opportunity.
I would like to see Barin brought back from exile (worth an episode or 2), I would like further attempts to try to get home (rebuilding the rift generator is bound to happen, either on Mongo, on Earth with Gordon Sr., or both). I'd like for the group (Flash, Dale, Zarkov and perhaps Baylin) to find a way to reach the construct moons and explore there. I wouldn't mind them eventually exploring other Mongo regions (which could be said to be deemed as too dangerous for intense colonization).
I'd love to see more of Rankol and his double-agent scheming.
Zarkov is my favorite character because of the visual and verbal humor he brings to the show but I seriously want to see the writers get him more actively involved in the adventures rather than just bumbling along after them. Toward the last 6 episodes or so, we're seeing some of this happening. In the last episode, he actually comes to Baylin's rescue, so there's hope for him yet to develop further heroic tendencies (at least a little more).
And wow, you are right. I wasn't thinking about Earth forces eventually invading Mongo. There's a thought. It's possible the writers may do this.