City design is by far one of the most important aspects in the game.  Without a properly built city, you will not be able to supply or build the troops needed.  I'll go into the resource fields first then later explain the whole inside goal.

Having a constant supply of resources is essential to building up an army.  There are two ways to go about this.  You can do the 50/50 route with iron mines and saw mills or you can go the 100% route with them.  You should only have one farm and one quarry.  Once your walls reach level 10, demolish the quarry and replace it with either an iron mine and saw mill.  The same thing goes for the farm once your relief station hits level 10.  I prefer the whole 100% route with all saw mills or all iron mines due to the fact that you get the largest bonus from valleys that way.  Doing this route does kind of limit you on supplies with the other if not done correctly.  When I say correctly, I like to place two towns near each other.  One of the towns is a lumber town while the other is an iron town and they supply each others.  Doing it this way can net close to 1 million per hour of that resource with a huge capacity limit.  If you do choose to go this way and are wondering which to choose between lumber and iron, the safe bet is always lumber.  Lumber will always be higher than iron on the market and lumber can easily buy you atleast 1.5x the iron.

Inside the walls is just as important as outside them.  The beginning town will need atleast one of each building except a warehouse.  Warehouses do not hold enough resources to be viable, plus the technology of Privateering lowers the capacity of them even more while being pillaged.  You should only have enough cottages to supply the labor force for the resource fields, every other spot should be barracks.  Each town should have a minimum of 12 barracks (this being a pure iron town and needing 9 cottages to fill the labor force).  While it is crucial to have a workshop, stable and forge in the beginning to get your technologies up, once the technologies that require them and relief station hit level 10, you can demolish all three.  This will free up three more spots for barracks to help train the troops faster.

The other aspect that I've seen multiple people make the mistake with is the use of Michelangelo's Scripts.  The scripts should not be used to upgrade resource fields until all else has been upgraded.  There are a few that should be upgraded first (and in the order listed):

Rally Spot

This is crucial to upgrade to level 10 first.  Each level lets you send out 10,000 troops so a level 10 will let you send out 100,000 troops in one shot.  90,000 vs 100,000 might not seem like a big difference but it can easily be the difference between a fight won and a fight lost.

Walls

Each level of walls give a 5% bonus to range of units inside.  While this also might not sound like much, it can be the difference between getting one free round and two free rounds against the enemy (a free round is when one side of troops attack while the other side is still out of range).  An extra free round can easily determine the outcome of the battle from a simple slaughter to being slaughtered.

Past those two, the next three are up to personal preference to which order they are done.  The next three that should be upgraded are the Feasting Hall, Town Hall, and Embassy.  Each upgrade here is pretty much self explanatory as they just add one more level of benefits.

Just to point out if you haven't read into the Heroes section yet, the Inn should be level 1 and stay that way (explanation is in the heroes section).