the biggest problem with tile limited cities, in my mind, is how deeply resources cut into your tiles. especialy on smaller maps where the rsources are much denser. if you have 3 resources inside your walls, then thats 12 tiles you don't get to use. this leads to very snakey cities as you try to avoid resources in an effort to actualy make use of your 50 tiles. I do not like this.
I think a far better method would be to limit cities economicaly. every tile increases a cities upkeep, so you can have giant sprawling cities... but they won't be producing any gildars and will likely be costing you some. idealy it would balance out to an ideal of having a handfull of moderately sized cities running at a modest surplus.
either way, resources should not count toward any tile limit, tile upkeep cost, anything. you cannot choose thier placement, and working around them can be quite frustrating.
I have to agree with using money to limit city size and city spam. Make gold more plentiful and easier to obtain. Make a tax rate that gives you gold based on population and each building or structure you build takes up gold to maintain. If you don't have the gold to maintain a building, you are not going to build it. Because cities can level up and get bonuses, this automatically encourages specializing your larger cities and NOT building tons of small cities because your buildings that you build in the large cities will get those city bonuses applied. You won't get those bonuses in smaller cities, so they are less worth-while to develop. This means you will naturally want fewer, larger, more specialized cities verses lots of smaller ones. But city level-up bonuses have to be available to add to each area of income - gold, arcane research, tech research, food production, mining, crystal harvesting, recruiting/military unit creation, etc.