Okay, dang it, this kept me up most of the night. It's IMPORTANT, really important, to get this right, and it's such a great new game mechanic, it would be a shame to waste. When people think of the highlights of certain games (MOMs "civ with spells", heroes, explorable lairs, differentiated races, AOWSM's hex, selectable leveling awards, tac battle improvements, height), it will be THIS game mechanic, the ability to place tiles in the city the way you want, that will be remembered for EFE (along with designable units). Other posts have made mention that Beta 2, in the second act, you start to make the decision about which way you'll win, but I contend that decision happens the second you found your second city: if it's by metal, or by a scenic view, or by a shard. Those things are rare enough that they will color your judgement about how you'll try to win from that very first decision.
So why not make city building support and enhance that decision? City specialization is going to fall along the lines of winning; it's GOT to. A city will either be a shard producer, or a metal producer, or a diplomacy producer (Horses/wargs straddle the shard/metal line; anything that uses units to win will benefit from movement enhancements). The choice of where to place tiles should reflect this, and maybe even should take a page from RTS strategy. If you have a special resource (like, say, metal) and you found a city near it, you should be able to build things (even multiple things) around it to enhance its output. In the city above, if you found near a metal deposit, you should be able to place mines (+20% metal, or what have you) on the 4 surrounding squares, and crank up it's production. If you put a study near a mine, it will only be half as effective, because who can read with all that clanging and banging going on? So, your mining city won't be your research city.
I'll sum up: I think the "limit of one per city" should be taken off for certain buildings (things that produce/enhance the special products of metal, crystal, diplomacy, research, mounts). I think the buildings that produce those, or enhance those, should have to be placed near the special resource to get the best benefit. I think that they should suppress producing the other types of special resources, so that a strategic choice for city development needs to be made. Finally, I think that you should be able to get insane bonuses for organizing the city in just the right way, so that the benefits feed off one another.
Tile placement should matter, and it should matter as much as the choice to make mages or diplomats in that city.
Oh, and since the word "diplomats" just fired off a neuron left over from Civ I, I think you should have units(or maybe champions) that can burn diplomatic capital to steal tech, magic, or units from opposing factions, but that's another discussion.
Winni "passionate about city tile placement, and doesn't want to see it 86ed" hym.