Fist off I wanna say that you guys have done a great job thus far turning the pokemon world into something that feels like an mmo. The maps are beautiful and the content is extensive. I just have a few suggestions that I think would further improve on what you guys have already done.
1.) Market System: I feel like the player controlled portion of the economy would work alot smoother if there was some kind of market-like function that would allow for players to post what they want to sell, and search for what they want to buy. The trade chat has been tested in other pokemon mmos which shall remain nameless. What usually happens is eventually players are forced to go to the message boards to sell their pokemon and items. This would also effectively turn catching rare and useful pokemon into a trade skill for making money. Trade chat, I think, should be just that, trading pokemon and items. It feels cluttered and chaotic with most of the people in trade chat selling things. I would work the search function like this:
-Pokemon
-----Type
-------Level
---------IV total
------------Shiny
-Items
-----Consumable
-------Berries
-------Pokeballs
----Non Consumable
--------Training
--------Battle
Im sure I missed a lot things, but you get the point. I'm an experienced Systems Engineer and I could flesh that out deeper and better if you need with a OV-1 diagram or something similar.
2.) Trade Skills: I've seen quite a few people in all chat say they weren't interested in competitive battling. There's a couple other things for them to do such as completing the pokedex and shiny hunting, but I was thinking of adding more fidelity and depth into the player experience. Most of these pokemon mmos have been centered around battling, which is cool because it's what most people do with their cartridges. What if however there was a way to attach a particular type of skill to the trainer (other than controlling pokemon of a certain level)? I was thinking of something like crafting skills (pokeballs, potions, items that help you find certain types of pokemon like fishing rods, bikes etc). Taking, for example, the pokeball crafter, you could require crafting items (held by wild pokemon or found by interacting with objects such as trees and rocks maybe) which would allow the players to craft pokeballs at a certain tier that are better, in some way, than the pokeballs you would buy from the mart. Here's a rough example:
-Pokeball Tier 1
-Pokeball T1 [Fire] + %[x] chance to catch success fire types
-Pokeball T1 [Grass] + %[x] chance to catch success grass tyes
(These item's names would appear green to indicate T1)
-Pokeball Tier 2
-Pokeball T2 [Flying] + %[x] chance to catch success flying types
-Duskball T2 [duskball bonuses] + %[x] chance to catch success
-Moneyball T2 + [x] pokeyen received upon successful capture
(These item's names would appear blue to indicate T2)
Again, if needed I can expound upon this simple diagram if needed.