At the moment, guilds are really nothing more than an extra chat, that aside from having more people to talk to has no real benefit.
It's honestly quite disappointing seeing how guilds are one of the staples of any good MMO, as such I've thought of quite a few ways to improve the guild system.
1. Extra guild positions: Namely Assistant Guild Masters, as a way to keep up with the guild when the Guild Master is online. Right now the burden of recruiting falls solely on the Guild Master, and if he/she is offline no one can join, this suggestion would be a great implementation as to assure that someone can be on around the clock to expand the guild.
2. Guild Levels: A guild leveling system is a perfect solution to the multiple people asking about a way to increase the max players, simply tie the max players to the level the guild is currently at. (Ex. Starting out at level 1 would be a 50 player max, level 2 would be 75, etc) Leveling the guild would be done by members contributing a certain amount of money to the guild.
3. Guild Shop: Putting money into the guild would give you a set about of contribution points you could then use to buy things within the guild. Which in order to ensure it doesn't affect the economy would be basic items you can already buy at a pokemart, and perhaps even certain guild-specific Pokemon.
4. Guild Bosses: A high-level boss the Guild Master could spawn with a high health that the entire guild attacks at once, whittling away at its health until it dies. Rewards would be based on participation, and possibly an extra reward for last hit. Rewards could be anything from varying sums of money to items like Rare Candy.
5. Guild War: Once a month, any level 3 or higher guild could participate in a Guild War, which is basically just a randomized tournament, and at the end the top 3 guilds are given certain prizes.
6. Guild Alliances: A way to expand communication between players. Once a guild reaches level 3 it can entire an alliance with other guilds, which would add an Alliance Chat tab to ensure there was always someone to talk to.