I have a few suggestions which could add more to the server and make it just a little bit easier on people, especially new users.
1) Beacons to show where the Pokemon healing stations are and the pokeshops. (As of right now the shops design are just red and blue, however in a few "cities" they blend in quite well and make it hard to see them, whereas having a beacon can show in the sky where they are and users can easily find them).
2) Frost-walker boots, an enchant that could be bought via tokens/coins or I suppose for the donating community. (Very simple idea, just allows you to walk on-top of water rather than ever falling into the water especially at snowtip mountains area.
3) Boss battles, this could be done via a cost, I.E $10,000 IGM (In-Game Money) to fight a boss such as that in pixelmon where the boss scales up by like 10 levels for a blue boss, 20 for yellow, 30 for red etc. (Meaning your level 10 Pokemon will fight a level 20, or a level 30, or level 40. Same for Level 100 Pokemon, will be 110, 120, 130). Or instead of cost have it as a public boss, however with the issue of anyone can battle it, may need to be more of an event that could go on, boss lasts for say 3 minutes and is spawned every X amount of hours, or done via a moderator.
4) Shiny Pokemon, having them on a chance upon catching to become a shiny, I.E just caught a magikarp, 0.0001% chance to turn into shiny. (As couldn't have shiny Pokemon to naturally spawn as anyone could then tpa them there and obtain them).
5) XP Shares / Stones / XP Elixir's / Lucky Eggs, Purchasable for tokens/coins of high quantity from such things as maybe the Mystery Man, this then stops it from be purely obtained through donating and gives those who can't donate a chance to have them. (This would possibly stop some revenue towards the server so most likely wouldn't happen).
6) Ability to see what pokemon you can fight/catch at the certain trainer level. (As you level up you unlock more Pokemon to be able to see/catch/fight, with this an ability to see what level you require in order to see a Pokemon would be a cool addition as you then know what you need to get to in order to see a Pokemon such as dratini, or snorlax etc).
TL;DR
Beacons for Pokeheal stations and pokeshops.
Frost-walker Boots for water.
Boss Battles.
Shiny Pokemon
XP Shares / Stones / XP Elixir's / Lucky Eggs
Pokemon level seeing.