Stacking food, much like stacking other resources, can save space. You could even allow the stacking to create new food items with higher value. Stack a banana onto an apple to get a stronger 'fruit salad'. Stack meat onto bread to make a sandwich. This new food item is worth more than the sum of the parts and can be sold on the market or used.
I've seen it in other games and it is very successful there.
Just a suggestion...
