Great suggestions. Some I have considered, and will be adding to the game.
Since I want this to keep to the period it is set in, the main crops grown back then were wheat, barley and dates. Barley became a main crop as the soil started to become more saline. But having a variety was necessary for both feeding the population and for trade outside. I also want this game to be a learning experience as well as something fun and hard to play. It has to be educational as well as playable (My next large project after I finish my Baseball/Softball Statistical System, with complete Sabermetrics, and be free and open source to all - and is written in QB64!)
As a teen, I spent my summers (and part of my winters) on a cattle farm in update New York (Liberty, NY in the Catskills), working a heard of about 200+ poll Herefords and a small string of horses (mostly used by us) on about 900 acres. we grew several kinds of grass for hay and 35+ acres of corn for winter feed (made for great pheasant hunting in the fall, as we left most of the stalks up with some corn on them for the deer). Even had chickens.
I remember when crows changed from being a bird we could shoot anytime of the year to having its own hunting season in NY. However, like problem deer, any animal that threatened the well-being of the farm, we were able to shoot year round. Some years we would instead of riding the fence line spend a week or two camping on the ranch on crow duty. My shoulder would be sore by the end of the day just from shooting at them. We even rigged M-80's in tree tops and lit them to scare them away! Those were the days. We never had luck using plastic owls. The crows sit on top of them and crap all over it.
Back to the game, I have done quite extensive research into the time period, so I will be introducing preventive measures for all kinds of pestilences based on how they did it during Hammurabi's time. I will even introduce a simplified version of their actual monetary system, as there has to be a cost of goods as it was back then, including costs of preventive measures.
I also have to do some work on the issue you bring up about rats. Yes, if the grain is sealed in clay jars, they are more protected from being destroyed, and I will be factoring that in. A good point.
But you know as well as I that introducing other animals to control others have their own problems. Chickens are easy, as if there are too many, they make a fine meal. Not so for cats, as their populations can get out of hand, and then they wind up wiping out all your free-ranging chickens! But such factors can be built into the game. I will have to reread my research on the methods they used to control pestilence as its been a while since I last looked at it.
We had plenty of dogs on the farm. I am partial to Australian Shepherds, and Daphne, my service dog, is an Aussie.
Thanks, great ideas, and I will be considering them.
As a farmer myself, I can give you a few ideas on a few features to add to the game.
1) A variety of crops. Potatoes, beans, corn, wheat, whatnot. Each has to have it's own unique seed and plant amount, and each will produce and feed a different number of people, as well as having different lifetime preservation times. Just because rats got into your cellar and ate your potatoes, that doesn't mean they got into your pottery and ate your dried beans.
2) With a variety of crops comes a variety of predators. Some of these predators can (and are) naturally edible as well, if you kill them. Example: Deer love to eat my corn fields. I love to eat deer. The natural cycle of nature makes us both get fatter with a good harvest.
Other animals are just pest animals. They honestly have no redeeming qualities to them, rather than to make a farmer's life hell. Crows, for example, are one of these species. Honestly, I'd rather have a whole swarm of rats invade my storage, than to have a murder of crows show up around my farm. Berries and such can, and do, end up stripped completely bare by a single flock of crows -- and often they destroy the harvest in as short of a period of time as overnight. I've personally seen whole orchards of cheery trees picked clean in just a few hours by a wave of crows that cawed and shit everywhere.
3) Pest prevention. Many of these pest animals can be controlled by the simple introduction of natural predators. One of the biggest deterrents to reduce insect damage to your crops is the introduction of free range chickens. Believe it or not, a chicken eats a ton of insects on a regular basis, and they absolutely love to wander around the loose soil of a garden/field. You have to keep them away from the crops until they're of suitable size to not damage them, but by the point that the plants have gotten large enough to leaf and bloom to draw insects, it's generally safe to allow chickens to wander amongst the crops.
Rats can be contained by adding cats. Crows can be contained by judicious use of a shotgun. (Just don't tell PETA or Uncle Sam. In North America, American crows are protected by the Migratory Bird Treaty Act. /CRY!!) Dogs do a good job of keeping many varmints away. (Which is why we domesticated dogs and cats to be our companions in the first place.)
Pesticides, fertilizers, lime and acidity are all things which you could add to a "can you feed your populace" simulation. Invasive species and species incompatibility should be keep in mind as well. For example, a walnut tree comes immediately to my mind, as my land is infested is thousands of the things. There's a lot of acidity in raw, unhulled walnuts, and when they fall from the tree, they turn the soil around it acidic. Any type of plant/grass that needs an alkaline base to grow good isn't going to grow near walnuts -- not without a lot of soil maintenance with adding lime to replenish the balance.