Well I was just thinking of a few small suggestions that might help a little (I'm not sure if they are already in or have already been suggested)
1.) Allow pokemon shared experiance kind of like on the game boy ones (ex. throw out a level 10 against a level 20 then call back the level 10 and throw out a 30 and beat the 20 and it splits the exp from that pokemon evenly between the two) would help with leveling up pokemon.
2.) Ability to see what skills do. (ex. skill growl says it lowers attack of the other pokemon. (this will help people who are new to pokemon know what it does so they dont think it does damage just to learn it does nothing more than lower attack))
3.) Ability to see what level a pokemon gets skills and evolves.
4.) The ability to see what pokemon can be found in what area along with a % of what the likeliness is of running into a pokemon (Ex. a cave (some command or item given to a char) geodude 50% zubat 900000000%(no one likes zubat and its by far the most annoying)) This type of command or item would help a lot when trying to catch certain types of pokemon.
5.) Donations, I understand the server will mostlikly need them to stay up however giving people something insane such as a really overpowered pokemon is a tad bit unfair. Perhaps something like a pokeball that catches a wild pokemon no matter the status of it so basicly a masterball. But just a suggestion.
6.) party up with another trainer so you can have 2 pokemon out at once kinda like in pokemon gameboy games and it splits the money and exp down the center however some kinda restirctions on it such as no gym leader battles or something.