I believe that khagan’s unpopularity results from the fact that only war and PvP are considered important.
For me, khagan is a crowbar and in combination with kunchen unbeatable. But my focus is primarily on singleplayer. There the heroes live long enough to develop their skills. If khagan and Kunchen stand together, khagan will use his ManaBoost to make sure Kunchen gets his turn quickly, heals his allies and lowers the enemy’s defenses.
Khagan/Kunchen is a guarantee that you will play through Atlantis hard very easily. If there is a Proteus next to Khagan besides Kunchen, the whole thing is a winning team, no matter what the other wing of your team looks like. I usually have Wilbur and Ceadmon or Sonya there.