I've thought about something like this, but just a bonus from a granary doesn't do much if all food sources tend to get it the same way.
I've suggested in the past special bonuses for different buildings depending on the resource (much like Stone is stone works, Mint is gold, silver, and copper, etc.). But it would be things like Sheep and cotton giving +1 gold if you have workshops (textiles), creating a bonus resource of Rubber that gives +1 production in Jungles and allows you to build a factory in that specific city if you don't have coal. Copper would be changed to a bonus resource that gives production or gold but still allows you to build a mint.
Basically, each resource might start similar, but it'll give you something different overall.
Sure, more variety is nice. I suspect that the reason for fewer resource-oriented buildings in this iteration is that the early-game build queue is already very full. If we're just tacking bonuses onto buildings that you'd probably want anyway (e..g granary, workshop), then that's probably OK. If we're building extra buildings (e.g. Stoneworks), then we're going to have building overload! How often do you get to build every Stoneworks, Stable, and Mint that you want to build? I almost never do.
I see the food resources as different flavors of the same thing. You get bananas in jungles, wheat in plains, and deer in forests, but in the end it's all just food and it all does the same thing. I'm actually OK with that. And why aren't cattle part of food?!
The mints for gold and silver actually bother me because most other luxury resources don't get any such bonus buildings. Sure, salt is more powerful than the others and marble gives you a small bonus to building wonders, but what about the rest? I'd like to see mint-like buildings for the others.