I usually occupy...

Maybe exterminate/enslave populations that are far from your capital and not likely to see much action or need to train large numbers of troops. You should probably look at each captured settlement on a case by case basis.

Of course, you can get around the tiny starting population by "importing" your own peasants and disbanding them in the new town, eliminating culture shock, reducing squalor in the first town, and growing the captured city.