Re city development & specialization & planning: how about some one-of-this-group-per-city buildings instead of or in addition to the 1-per-city and 1-per-empire buildings ?
One group would be consist of buildings with some % bonus to gildar / tech research / arcane / food / recruitment speed / mining / shard harvesting, etc.
There might be a 2nd group with fixed-amount bonuses like +10 tech research, +10 gildar, etc.
Any city could have one from group 1 and one from group 2. If I tried I could come up with a third group.
For best results, using tech as an example, find a lost library, build a city near it, build as many studies/libraries there as you can, pick the tech buildings for both group 1 & group 2, and pick tech as the specialty when leveling-up. Also, of course shovel in a school and university if those remain, but I suspect at least 1 would be re-positioned as a one-of-this-group tech building.
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A whole different approach: focus on the level-up bonuses. Add options for farming bonus and "nothing" in addition to the tech/arcane/gildar options, and proclaim that ONLY ONE city per empire can get each bonus. Ordinary cities get 'nothing'. That's for level 1 -- for other levels you are locked in to what you picked for level 1. Then they might need to re-balance by making the bonuses bigger, or making some building like schools help more.
I don't like this a much, but it might be easier to implement.
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Yet another approach: in addition to the old 5-square limit on how close suburbs of different cities can get, forbid founding a new city with its center less than maybe 20 or 25 squares from the center of any existing city. That largely kills city spam and indirectly makes planning / managing the relatively few cities you have more important.
I think they could actually do all 3 of these if they felt really ambitious. Right.
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Meanwhile, re Brad's original idea on population costs, from his 1.29 beta log post "LOTS of code to handle the increasing costs in terms of people to run your improvements. If anyone thinks that getting highly talented people remains equally easy as you grow, ask google, microsot or apple about that. It's not."
... he wasn't perhaps projecting a bit, possibly traumatized for life by what he has had to pay to attract talent to the frozen northern wastes ???? 
It might have been easy at first, hiring locals who had been to programming school but didn't want to move to silicon valley or Seattle, but once he has to start paying people to move a place they don't really want to live -- yikes ! (southern Kaliforniac here, letting my climate prejudices show)
BTW "microsot" ?
