Disenfrancised
Beep Beep
The buildings which I rarely/ever build are the tanner (never - the health penalty is a killer for those small bonuses), the weaver, the brewery (sometimes one or the other, but they're very low priority), and the coffee house. I haven't played many games which ran late enough for the coffee house, but I rarely have happiness problems even with 20+ population cities. It seems like we could eliminate some of those without taking much away.
If we're interested in adding the well, we could make it available with the same tech that makes quarrying possible, and give it either the same function as the herbalist (possibly making the herbalist much more expensive, and giving it a +2 health bonus?) or make it much more expensive and give it a +2 bonus.
If we really wanted to make it interesting, we might make cities with wells more likely to get plague, to represent outbreaks of cholera and typhus.
Health being the limiting factor to growth is rather realistic for European cities.
For Northern Europe the brewery is pretty useful - its one of cheaper ways to get quick happiness before the Colonial Era, and generally the first happy building I get once all the religion buildings have been built.
I do like the philosophy of every resource having two buildings that provide a bonus, but I think it'd be better if they were slightly more distinctive and varied than the +5% commerce.
Another possibility to explore is having more unhappiness penalities to mitigate the happiness surplus most cities get - have certain civics generate unhappiness (say Beaurocracy gives +1 unhappy in every city without a palace for example), and the +XP buildings give unhappiness (to show the citizenry's dislike at being recruited/pressganged and hard trained) so you don't just build them everywhere.