Ill try to keep it short:
There would be a system where you can make your own base(For your guild, obviusly) and making this would cost $$(1m++, it needs to be a very end game objective for guild cooperation, maybe 10m so everyone on the guild has to contribute to be eligible to enter the ladder guild system?, need suggestions here)
After making your base you will be able to participate in the guild ladder system, where you can "raid" other guild's bases and if you beat their base you will win points which are going to show on the guild ladder system, the base would cost a lot of $, and winning points on the ladder system will let you get items for your base(decoration) to show your dedication, also, you will get ranked as a guild.
Obviusly this need a lot of work, and a lot of things to add, but this is the initial suggestion and i plan on making a very detailed edit on this post after your criticism, so we can make this a better suggestion.
Edit 1: Maybe on the guild base, after beating a lot of other guilds and earning points you could be able to buy a spawn zone(having the same rarity of other zones, but on your own base so you dont have to travel, i.e: having route 104 on your base on kanto, so you dont have to go to hoenn)
Edit 2: Im having trouble on the guild ladder system, thinking about it, to raid a base there would be a queue system(like for individual ladder) and you will enter with 3-6 members of your guild, then get in queue and if another guild is in queue you will be put in your/their's base and will be fighting eachoter, whoever wins gets the points(Needs suggestions here)
Edit 3: So thinking about it, guild bases would be the start for this, and you can have decorations for them, the problem is that without the guild vs guild system there would be no points to get via pvp, so maybe there should be guild quests(where every member contributes with X points) and your reward would be guild points(GP) and with these you could buy decorations, also, you could buy guild zones(route 1xx i.e, or a direct transport to that route and viceversa)