i've been playing for quite a while and i have some suggestions:
1. contests: adding this option would make PRO much more fun, mostly because people would not only have moves based on usage in battles, but also in contests
2. double battles: i haven't been to hoenn region yet, but i have not participated in any double battle yet (and i simply love double battles)
2.2 double battle with other players: it would be awesome if there were not only 1v1 battles but also 2v2 battles
3. auction (i believe people are already working on it): instead of just regular trading system, there should be a place where players gather and they can have auctions... for example: someone offers dragonite and it is given to the player that gives the largest amount of money or the best pokemon
4. tournaments: even though PRO is a multiplayer game it is quite individual, because you can only interact with others via chat, trades and battles... i think there should be a place (like battle tower) where players gather and they have a tournament (the same system as for example uefa champions league, where some players (128 or 64) compete in group stage and then in elimination stage... i think that that would be Quite hard to make, but it would be a great improvement
5. breeding... i do understand that breeding has been suggested before and that these requests were always denied, but how is breeding not a thing... i agree, there should be no daycare centers, but breeding... some pokemons (mostly baby pokemons) are usually obtainable only via breeding... of course ditto and x pokemon shouldn't level up during breeding...
6. new regions (that's more of a question than a suggestion): first of all, congrats for hoenn region, but when can we expect sinnoh or kalos?
7. better pc: (that has already been suggested) a pc where you can search for pokemons you've caught, and you can also sort them by type, (height, weight), level