What about making certain building classes available in cities that have >= a certain population?
That way if you want to have a buildingclass that does something great, you need the population to warrant it!
At the moment it is sort of implemented in the mechanic for arenas, colossae, theatres, etc. in that the effect of producing happiness kicks in only upon reaching that population level, but that is only for the counter-unhappiness effect. If we had it on buildings that aren't just 'happiness generators' then the reason to go 'tall' is obvious.
To counter that we could also make a buildingclass, or group of buildingclasses, that can only be built if the empire has >= a certain number of cities.
The two sets of buildingclasses would be similar in outputs, but different enough to make the choice a difficult one.
So you know that if you found x cities you can then begin building these types of buildings that grant you y bonuses but if you go tall another group of buildings gives you z bonuses, which may or may not match your goals at the time.
A bit of code would be needed to do a check on these cities so that if the 'wide' buildings exist the 'tall' ones won't be available once the city grows. Or they are lost and the 'tall' options become available.
Hmm... I'm just pausing over this before I submit it and it may be overly complex and not even hit the mark. Doubt washes over me.

I think I may have just reinforced one of my pet hates about 'tall vs wide'.

This all depends on defining a certain number as the difference between wide and tall. Ah well, it's just an idea.
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