Here are a couple ideas I've been thinking about.
1. 'Debuff'/'Buff' animations are too long.
What I'm talking about here are the little blue particle effects that shower on a pokemon after they've been hit with a move like growl. Or the animation when they buff themselves with something like focus energy.
Okay so in the original games, this animation exists to show players "hey this move has reduced your Pokemon's stats in some way. Maybe you want to read the chat log to figure out what it's done"
For new players to the series, it makes some sense to have an animation like that. But PokeMMO is not something that's really aimed at newer players to the pokemon franchise. I would wager that a vast majority of players already understand debuffs... So I think seriously shortening the animation would be beneficial. It would still be there to inform the occasional new player... but for everyone else it wouldn't be such a time consuming ordeal.
Especially in the earlier parts of the game when you're fighting lower level pokemon and combat goes on for 3-4 turns. To have a pokemon use tail whip on you over and over, it feels agonizingly slow to watch that debuff animation play. I also personally (and I imagine some other people feel the same way) find myself wary to use buff/debuff skills when not absolutely essential because of how long they take. This could be something that both speeds up combat, and makes certain underutilized moves seem more appealing to users who are concerned with speed/efficiency (which is a core part of this games audience)
2. Speed up of the zooming/pokemon-movement during skills
Okay so I should clarify what I'm talking about here. Anytime you use an attack, the camera zooms into the target, or the screen will change colour, or the attacking pokemon will move etc to give you a better view of the animation. This is great, it makes the visual effects pop, and it's important; however, I do think these animations could be sped up to increase the flow of battle.
3. Speed up screen transitions
Not much need to explain here I don't think.
Just increase the speed of battle transitions, calling out your pokemon, etc. They're pretty slow and repetitive, and one of the most noticeable slowdowns in combat.
Overall pokemon is a game all about battling, and everything supports that core system. There are things like breeding, IVs, EVs, etc... but they all serve the purpose of making better pokemon for the sake of battling. So I think it's very important that battles be made a smooth, fluid, and responsive as possible and as good as it is so far, I think there is still room for improvement on this front.