Quite a few great ideas here!
Lyceum - that sounds like a good one to add.
War Council - sounds like a great choice over Tower, but I think the numbers need to be different, either 5/5% boost on attack power/battle experience or 10% boost on one or the other, but a good selection to pick over tower if someone wanted it.
Library - I like the resetting points for free, but should have stipulations on being able to build it, like senate must be level 25, and it takes quite a bit longer to build, days even. I am saying days because what it would do is something that would normally cost you CP, so no matter how long it takes to build, it is still worth it to get it, just for a brief moment.
Lighthouse - I like the 25% speed boost recommended for it.
Theater - either lower the time it takes to run, or make it longer and double the CP you get for it.
Statue - a bigger temple boost would be a nice upgrade for this one.
Gold Mine - Not real keen on this idea, because it gives free gold. I think if it is going to do that, there has to be stipulations to getting it, like resources must be put into the gold mine daily, meaning you have to check in daily to the game in order to get it, and kind of leaning more towards it being a once weekly collection instead of a daily collection, where if you miss a day, you lose it and have to start over.
Oracle/Thermal Baths - don't really see much that needs to be changed on them
Merchant Shop - maybe put a speed boost on the resources sent from that city to others, but otherwise I think it is fine.
I feel like i missed some, but I do not think we need to add anymore items that would increase population of the city. If there were to be more than one of these, then I feel you should only be able to pick one of them per city to use.
Some of the ideas put out there, why could they not be additions to what is currently in the game?
Aqueducts/Cellar/Diplomatic Center/Acropolis/etc. could be add ons to existing buildings, I think, with a bonus attached to them, and a limit on how many add ons you can put on per building would be your limitation.