I'll be piling up many suggestions under this topic with the knowledge i gathered about the guild system so far.
Self Sufficient guilds : Similar to the ranking system, where guilds needs to battle in order to improve both their bases and equipment inside. (cosmetics, building space, rooms etc.)
Guild base training areas : Inside the guild, there should be several rooms for training purposes, namely EV's. Gathered from the information in hand, pokemons that are spread out far too wide for having a specific EV training areas. Ofcourse these rooms will be in hand-to-hand with my first suggestion where they will be unlocked with battle point currency.
Battle points : Each point will be earned by defeating another fraction/guild. Every win will give you 2 guild coins and can be donated to your guild bank. Only the Leader of the guild and the ones he chose will be able to use those. Battle points will also require for you battle in "Guild Mode" and these points will not be able to be traded among other guilds.
Custom Battle Island : For future events that are going to be held. An Island which will have an arena and special shops that will allow players to rent/purchase battle items (leftovers, black glasses etc.)
Hall of Warriors : Inside each guild, will have a throne room to display their trophies and achievements for public display.
Guild bases : Players should be able to choose where their bases will be (I.E. Viridian : Available guild spots : 1/4) Each guild location will have a certain pokemoney range based on the city they're in.
King of the Hill Island : Only the guilds who have achieved a certain ammount of chalanges/tournaments will be given access to make their bases in this island with more base space and for their own advertisement.
If the guilds have the same ammount of achievements and another guild has already claimed the island for themsevles, a guild war will determine who will claim the island as their domain.
These suggestions are not of high priority or required to be implemented. They will simply take the end-game to a whole new level, namely promoting battling and teamwork to improve. Most of these will require game to be developed to a certain degree to meet the requirements this suggestion needs.
Some of these may already have been suggested, i didn't have time to go through every suggestion that was made. Credits belong to those people if they have already suggested.