A few comments/questions and things that I would like to be changed.
1) From what I've read, it appears the warehouse can be located like a city in the game. I believe a simple change so that the warehouse is just a warehouse, where you can send resources to would be much better. It'll be located somewhere on the map by entering the coordinates and it's kind of just there. You can move it if you want to suit the needs of the alliance, but moving requires a reduction of 25% resources in the warehouse.
2) I don't like the pillaging of the warehouse by other players part, just make it an alliance only function. You just send resources to it and may withdraw resources from it. Allowing the warehouse to be attacked complicates the idea too much.
I have included these features for reasons of balance. If the warehouse can't be pillaged, then someone could just send all of their resources to the alliance warehouse, where there's no danger of it being stolen. After that, they could just extract the same amount of resources, or request a leader to give the resources back. It just opens up too many abuse possibilities.
I will however raise the amount of resources hidden to 25%, and the amount needed to change 25%.
3) "There will be an alliance warehouse, which can store as many resources as the alliance has points." This has to change. Alliances can have several million points and it's just too much. Effective resource management is important to this game. So put a resource cap on the warehouse.
This raises an interesting point. Maybe the amount of resources could be capped at 1m.
4) A marketplace is required. You send to it as if you're sending to another city. Get rid of the part that says "You can contribute to your alliance warehouse without a marketplace, but can only give 500 of each resource within 24 hours." It over-complicates the idea.
Okay, you will need a marketplace.
5) Where are the visual aids?
6) "They can also regulate transfers to other alliances via the same screen" - Don't make it some sort of inter-alliance warehouse. Leave it as your own alliance only.
Transfers to other alliances could happen anyway. A founder(who sets access rights) could give himself 100% access, take a huge chunk of the resources away, then transfer them, bit by bit, to another alliance founder. That founder could place it in their alliance warehouse. I will add that you can only transfer to another alliance once every 24 hours.
7) Add that you cannot cancel any outgoing shipments, also if the warehouse overflows, then you lose the resources you send to it.
Added.