How about all unused tiles produce food (a variable supply depending on the tile and/or planet type) as long as you don't build on them. Some improvements could increased the food they produce.
So basically, almost everything is arable land, to some degre. Just like in real life, actually. Settlers can do basic farming on every tile of the planet, as long as there isn't infrastructure occupying the place. Then, some buildings can represent the infrastructure needed to produce greater amounts of food.
That's a good idea. It combines food as a background mechanic (mentioned earlier in this thread) with a new strategy:
Not building something increases surplus food.
It seems like that would be easy for the AI to handle too.
I really like this.
I think it would be good to include a global mechanic that Food Deficit = starvation = population loss. Those Farming planets are great, but if you lose them you should suffer big time.
So the biggest change is that Cities and Megalopolises should not cost food to build.
Population should be dependent on food supply. Cities only allow your population to grow larger.
I would also add that upgrading the basic farms should use Thillium or Promethium or one of the "space" resources while the hub buildings use monsantium or unique stuff. You don't need the hub buildings, but the current system is so very unbalanced.
That are good ideas, but I have some adjustments:
- Unused tiles produce food according to the planet type. Desert planets less than terran planets. But only so many unused tiles are taken into account as there are other improvements on the planet. So a freshly colonized planet would only get the food from one tile. If you build another improvement, two unused tiles are taken into account and so on. That prevents freshly colonized planets to produce large amounts of food instantly.
- Food production should be a continual process (like mining other resources), cities and the like should not need food to build, but the population should consume food every turn according to its size. When there is not enough food to feed everyone population growth on all planets should become negative in relation to the amount of food that is missing. Also morale should suffer a hit (perhaps -1% globally per turn food is missing). Don't forget to implement recovery from that morale hit once there is again enough food 
- There is no base production of food based on planet class. So to colonize a new planet you first have to make sure you produce enough food (or have stored enough) so that your new colony doesn't begin to starve immediately.
- Food can be traded with othe civs (or sold in the new galactic market coming with the new expansion).
- Introduce agricultural modules for economic starbases.
- Introduce (upgradeable) hydroponic farms to produce food on tiles that are to harsh to grow anything naturally.
- I agree that standard resources become more and more useless as the game progresses. I have modded my game so that some improvements have very high standard resource costs, so I actually have problems to build enough mining starbases (administrators are limited after all). And I began to put in missions that cost a really lot of standard resources (like 50 or 100) to get special resources like monsantium.