Wow, that looks truly amazing. It's awesome!
It would work perfectly that way but I think we'll certainly need more types of bonus resources. I think a lack of bonus resources will become a big problem otherwise. It's also just more fun to have more bonus resources
I agree with everything, it's just the penalty for unhealthy cities I'm not so sure about. It seems very much like the unhappiness penalty. It makes sense ofcourse for unhealthiness to lead to population decline, and it also makes sense for unhappiness to lead to population decline. Still, I've got a bit of an out-of-the-box idea to seperate the two.
Disease
Let's keep the unhappiness penalty for what it is. But when unhealthy, cities don't have any direct penalties. Instead, there is the risk of a disease being created. This will be based on chance and depend on the amount of unhealthiness. (for example, if you're 1 health short it's 1% per turn, if you're 10 health short it's 10% per turn, etc.)
When a disease starts in a city it will cause that city to lose 1 population per turn (simmiliar to being razed, without the anarchy). The disease has a chance to spread to other cities within 10 tiles (like religion), this chance is based on the health of that city (for example +10 health, 0% chance. +5 health, 12,5 %. 0 health, 25%. -5 health, 50%. -10 health, 75%. -15 health, 100%.)
A disease in a city also has a chance to end ofcourse, this also depends on health. For now I used the spread chance and inverted the formula. (for example +10 health, 100% chance. +5 health, 75 %. 0 health, 50%. -10 health, 25%. -20 health, 0%.)
So what you get is simple. Being unhealthy has no direct penalty, however you run the (fairly small) risk of a disease starting. A disease will cost you alot of population, and can be a huge hit for your empire. It will spread to other cities overtime, especially unhealthy ones. But it will end at some point, also based on healthiness (or a city running outof population and being razed, which'd be extremely rare).
Basicly, taking the risk of going into negative health may be tempting, the chance of a disease starting is only small. But when a disease has already broken out near you, you will want all the health you can get to keep it away from your cities, or at least get it out of your cities faster. There might also be diplomatic effects (''a disease broke out in your empire'' or ''a disease in your empire spread to my empire'').
Obviously, diseases can do huge damage to unhealthy empires, and it certainly can be triggered on purpose to spread it to other empires (though that tactic is costly and easy to counter with bonus resources).
PS: although I wasn't convinded of a first expansion being made, I am convinced a second expansion involving bonus resources and health is planned or has been planned at some point. Bonus resources seem to be begging to be used for such a purpose.