I'm all for city specialization, but I'm not a fan of its current implementation. Making one city with 20 +1 research buildings and another city with 15 +1 arcane buildings and another city with 10 +1 workshops and great mill, etc., is just not all that interesting.
Here are some ideas to make it more interesting:
Cities specializing in research could do something like this:
+1 research study (applies to general research ... this already exists today)
+1 civics research study (bonus applies while researching the civics tree only, think of a better name and have this apply to all tech trees)
+10% schools (general % uplift across all)
+10% civics schools (bonus applies only to one particular tree)
If prestige worked a little differently, you could have prestige attracting certain kinds of heroes. For example, a college might create "research-type prestige" which would increase the chances of a scholarly hero hanging around town wanting to join.
If heroes worked a little differently, you could employ that scholarly hero in the college (not just the city) to give that building a research bonus.
Each of the resources could have alternative buildings too. For example, instead of harvesting a shard for mana, we could put a lab on it to study it for arcane research. Instead of mining stone, we could put a lab on it to increase weapons research, etc.
Anyway, just some ideas to spice up city specialization which I really like as a concept but don't think any game has really ever implemented it well. Most of the time city specialization just means "build 1 kind of building and don't build any others".
You could do something similar for cities specializing in magic, troops, materials, etc.