Even after the newest update, the issue with Battania just steam-rolling through almost feels worse. I started a new game while at work yesterday, and not even 2-3 hours into the game, they had essentially wiped out one of the Empires. I restarted (SAME shift) with a whole new character, and lo' and behold, they did it again, again - less than 2 hours in. Both times they began their conquest by going for the same city, clear on the other side of the enemy kingdom.
I started to watch and noticed that the defending kingdom didn't seem to react much. Unlike in Warband, where you'd see a bit of tit-for-tat going on or nations would immediately attempt to retake their lost city, it just looks like the lords are riding around not doing much of anything.
I'm not sure what the 'solution' is, but I guess I could throw out some ideas.
Newly captured cities should have a high degree of unrest, requiring resources to control. If unrest becomes too high, various events may be triggered, such as riots (self-razing), revolts (an attempt to flip back to the original kingdom), and treachery events. Those might range from everything from "assassination attempts" to creating back doors for recapture sieges (giving huge bonuses to the original kingdom).
I also like the idea of the 'homeland' of a conquering kingdom to become unruly if the armies are spending too much time outside of it, including the spawning of new factions.