Not a bad idea honestly, adds competitiveness within guilds.
But there are a few things in your suggestion I believe need to be changed, or shouldn't be implemented at all.
1. I agree totally on the ladder.
2. This would get touchy, I don't know how much guilds would actually participate. I know this will probably result in more PVP focused guilds being created though.
4. I agree, though I don't agree with challenging, I'd like to see more Ranked PVP matchmaking type system.
5. I agree with immunity, but I don't agree with it costing poke $, or coins etc. It should be free, considering some guilds don't PVP.
6. Enemies would be fun, but would need be tested in my opinion, it could go bad if not implemented correctly.
7. The battling needs to be fleshed out more, feel its to bland. And that wouldn't work. I could be wrong though.
I agree completely with rewards aswell.