It would be really useful if there was a sort of 'not' function for bonuses, particularly relating to city upgrades, that would allow for things like:
Preventing the building of a certain upgrade after a designated tech is reached,
Preventing the building of certain upgrades if you own a particular hero,
Presenting a hard choice between two powerful/unique upgrades (Do I strip mine my empire or provide land for farmers for example.)
This would be really good for city upgrade mods, and in general just allow for a lot of cool stuff.