While I believe the recent changes to rationalism (and its related cards) was meant to encourage players to grow big cities, I think there has been plenty of evidence presented that at best there exists a small incentive (and a big opportunity cost) to do so. Here is a very simple solution to this problem. Tier 1 buildings require 5 pop to build. Tier 2 buildings require 10 pop to build. Tier 3 buildings require 15 pop to build. This would also significantly slow down research which is imo desirable.