I think that the timer is a good thing, in RTW you should be able to take pretty much any city in 40 minutes. It shouldn't take hours to take a city, in my mind. Everything is scaled down in RTW. There aren't 256 man phalanxes or groups of 10000 legionares. The fight time on unit-to-unit fighting is shorter than in real life too. So it seems right that the time limit for taking cities is scaled down as well.

However I do hate it when the enemy has a unit of horse archers and just run away from you until time runs out and you lose the battle.