Since TL;DR, I'm going to put an idea up front:
Here's an idea - once that tipping point is reached and the game can tell its toast.
- A mega hero arises and unites the opposing nations - both empire and kingdom
- For the next X turns he and his band are traveling to super spiffy mountain to do something heroic
- Upon success the hero and all surviving (some could heroically die) sidekicks get more powerful
- If not stopped, for the next Y turns he brings the thing he got by being heroic back to a random city.
- If not stopped, for the next Z turns he consolidates power, the hero and all the surviving sidekicks get more powerful
- If not stopped, the hero and surviving band chase the Sov down from the random city to wherever the Sov is (somehow cloudwalk becomes mysteriously disabled)
- A final fight ensues - with the winner claiming the world.
- Ta Da - holy crap end game

Note: Probably have X, Y, Z and "gets more powerful" and/or # of sidekicks determined by difficulty level.
One other factor that is critical and mentioned above - I have a 4 essence Fortress that I've put +production, +initiative, +attack, +hit points. Its my only fortress, why would I want to build units anywhere else unless in drastic need.
But ANY unit built in that fortress is going to have:
+3 move and +3 attack (level 2 upgrade) - which I personally think is better than "go first"
+25 damage to damaged units (if I ever get to level 3 I think)
+4 initiative
+4 attack
+4 hit points (which is rare since I usually play empire)
So even if I build a base spear dude late game, he's going from 6 to 10 attack, 6 to 10 hit points, and 20 to 24 initiative...
Needless to say I'm going to build my units for initiative and attack and only put on enough defense that doesn't impact my initiative.
I'm going to put them on a warg for an extra +2 initiative
I'm probably going to spend the crystal to give them +1 initiative
I'm going to spend a trait to give them +2 initiative
Another trait to do +15 weight and +1 attack to free up some encumberence (not that you can see it anymore)
I'm going to use my 3rd trait to give them +3 attack for anything less than my probably 29 initiative
Then first turn I have high initiative, extra attack and movement - and will probably go twice compared to the AI.
How is the AI supposed to compete with that?
I've also focused my production and I may be able to spit out a high defense attack machine in a turn or two once the war machine gets rolling. And one of these units can usually wipe the floor with multiple NPC units - if not a whole stack if up to light plate/chainmail.
First turn is KEY, especially with multi hit units (cleave, impale).
Initiative is dangerous. I don't think it needs to be capped, but I think every unit should have an action every turn.
Charge is dangerous. I don't think it needs to be nerfed, but we need anti-firstmove traits. A la, on first turn prevent enemy from moving more than 1 tile to come into contact (hard to explain, but if 8 away, can only move 7 on first turn.. can't charge right in). Call it spearwall or something. Maybe require spear.
Swarm is dangerous. Not sure it needs to be nerfed, but should have anti-swarm mechanics.
I also agree late game could use some work.
PERSISTENT METRICS - to compare game to game
Better boss fights a la OP
Some better way to finalize/kill a civ - needing to clear each individual city is just too much drudgery.
Was it galciv that had the mechanic that if an enemy felt they were overmatched they would surrender to someone and it might not be the person beating on them? i.e. They lose a few major battles/cities and realize they can't win.. they throw their lot in with someone else.
Might have actually been EWOM, can't remember but vaguely remember it might have had to do with dynasties.
Here's an idea - once that tipping point is reached and the game can tell its toast.
- A mega hero arises and unites the opposing nations - both empire and kingdom
- For the next X turns he and his band are traveling to super spiffy mountain to do something heroic
- Upon success the hero and all surviving (some could heroically die) sidekicks get more powerful
- If not stopped, for the next Y turns he brings the thing he got by being heroic back to a random city.
- If not stopped, for the next Z turns he consolidates power, the hero and all the surviving sidekicks get more powerful
- If not stopped, the hero and surviving band chase the Sov down from the random city to wherever the Sov is (somehow cloudwalk becomes mysteriously disabled)
- A final fight ensues - with the winner claiming the world.
- Ta Da - holy crap end game

Note: Probably have X, Y, Z and "gets more powerful" and/or # of sidekicks determined by difficulty level.