1- Use the server correctly. This "Announcements" section is the most useless section i have seen in all forums i have participated. 11 hours server down and 0 informational threads in that section (Announcements is a specific section for news and server issues).
2- Ingame chat punishments. People spam and insult in chats, but the best thing you can do is 60 seconds mute. If you want to use a mute punishment make punishments harder, (like 1st warning: 3 ingame hours mute, 2nd warning: 6 ingame hours mute, 3rd warning: 12 ingame hours mute, 4th warning and above: 24 ingame hours mute, and a warning reset system, i.e. If you have been 1 day without receiving a warning, your warnings are reseted). I'm tired to see the same people muted once and again. They will never change with 60-90 seconds mute, and you won't get a clean chat with those little punishments.
3- A decent pokemon storage system, just like the official one (different and configurable boxes + a favourite system for those pokemons that you don't want to lose due to a mistake by oneself, i mean, fav pokemons that cannot be released/traded).
4- F2P mount (1-2 are enough imo), completing a quest, after 8th johto badge, for example. (I don't know if it's actually possible to get a free mount completing a quest)
5- One of the most important things in my opinions: Punish the use of "cry" and "noob" words. These words are disrespectful. Noone "cries" and noone is a "noob". Some people are newbie, and some people discuss and complain about things.
I will update the thread if i think in more useful suggestions.
Excuse me if I make many misspellings.