I pick Engineers because their base 80 engineering gives +20 production, which is as good as the Boost bonus in Castles and still pretty good in towns.
There are a couple other cheap perks that are good and fairly easy to get as well. 50 Riding gives +1 prosperity, 50 polearm gives +1 militia, couple others. Just give them a glaive and send them at looters. Athletics and Bow are really easy to level and have some good ones if you want to put the effort in, just keep them in your party on foot with your archers and they'll level. Helps if you hire them early before you get fiefs so you're not spending time leveling them instead of having them govern.
Far as daily defaults go, Irrigation is pretty powerful. Turns each point of production into .01 hearth growth in all bound villages, which adds up when you've got 200+ production. That's five times the normal rate of village growth, and more growth means both more flat food bonus (+5/10/15/20 at 300/600/900/1200 hearths each) AND more tax and production, which if they produce food also massively raises your ability to grow town prosperity.
My strategy is to get everything useful built, then go Housing until my Food Bonus for Prosperity drops below +1 or so. More prosperity gives more base production, so it's best to cap it out because it makes the other daily defaults more powerful. After that, go Irrigation until the villages hit the next tier, giving more food and letting you grow prosperity again.
The thing I don't like is that some cities just will never amount to anything no matter how much effort you put in. If they only have two bound villages and none produce food, they'll just never be able to be as profitable. Jaculan and Marunath are two of the best cities to have for this reason, 4 villages each and tons of food so they can theoretically grow forever if you do it right. Marunath is even better because the villages have the +1 militia Battanian culture modifier, so one you get them to 700 hearths or so they'll have over 100 militia so most normal-sized enemy parties won't even bother messing with them.