I don't like the fact that a couple of my cities seem to be bottomless pits of money-loss, I can't figure out how to make em gain money. But most of my cities make a little money, so I don't lose money over all.
This is because the upkeep costs of your armies are divided among all of your cities according to population levels. For example, a very small town may contribute only about 1% of the overall upkeep cost, while a large city like Rome may have to pay 10~20% of the whole upkeep cost.
You will notice that the income for that city actually rises when you create units, while the income of the cities nearby drops; this is because by creating a unit you are conscripting from its population, so as the population drops a bit, its share of the total upkeep cost also drops a bit.
At the same time, the dropped amount of upkeep share from that city(plus, the new upkeep for the units you've created), is distributed among the other cities, since the relative differences in population dropped.
So its not really something to worry about. Having a city that goes minus income just means its a large city that spends more resources than produces, and having a city that earns big money simply means its a small town that produces more than it spends. If the treasury remains positive, no problems at all.
The battles are great and the new 3D units good to watch, but I can't help but think that everything moves a bit too fast especially compared to MTW's batles. One thing that's good to see is how effective archers are. MTW I never use to bother with them other then Lonbows. Archers in RTW are awsome.
Some people hate the new speedy element, but I myself love it.
The following is all my personal opinion, but..
MTW was way too slow. The multiplayer battles of MTW was "form a battle line, send archers, go grab a cup of coffee". You could just leisurely watch the enemy trying to do something, and then think out a plan and go block their move.
So in MTW, it was usually a matter of who formed a better formation, and who had better archers. A stagnant fight between long range units would come first, and then the period of "long silence". Usually the guy who breaks his ground and starts to attack first would lose.
However, in RTW its balanced out to the middle point - everything is faster. Cavalry is fast and powerful. A slip of a concentration and the enemy player will start flanking you. Unless you react just as quickly, or have a better plan than his, fighting passively in MTW will make you lose.
The keyword of RTW is "initiative" - you need to grab it first, react to things more quickly, and makes the enemy do what you want him to do, instead of waiting for him to make a move and then matching it.