- Scale wild pokemon levels closer to the player's current strongest pokemon in their party, or alter the spawn rates so higher level pokemon appear more often than weaker ones, relative to the level of the player's team. Having high level pokemon in the wild adds some desired challenge, but there should be some degree of scaling to balance out gameplay. Early game players can currently spam pokeballs to capture high level pokemon without much effort, and low-level pokemon make for poor EXP sources for the late game.
- Make Pokemon PCs easier to craft, because currently it requires a diamond pickaxe to make a nether portal to even get the ingredients for the redstone lamp. I recommend adding silicon as an ingredient, to make silicon more useful. I suggest this because I've played quite a bit and have only found ONE Pokemon Center with a PC in it. The dozen others I've found have none. PCs should also be readily available because the actual Pokemon games have them all over, from start to finish.
- Increase underground pokemon spawn rate. I feel like there aren't enough of them underground to make mining and underground exploring more interesting.
- Increase likelihood of wild pokemon avoiding towns and player structures, and prevent them from spawning within. It seems kind of silly how pokemon spawn in or waltz right in to towns, and some will randomly attack the player while they're focusing on, say, building.
- Give Mechanical Anvil the ability to hammer aluminum into plates. It seems more logical and convenient this way, though it would make the Pixelmon anvil eventually obsolete (as a side note, the Pixelmon anvil should be renamed, since regular Minecraft already has anvil for combining weapons, etc)
- Eliminate or reduce fall damage from mounts (with Drifblim especially, though other Pokemon mounts may have this problem). Riding on non-flying pokemon (i.e. Feraligatr) and taking damage from short falls makes the feature less desirable.
- Make town NPCs useful. Item or Pokemon trading with some of these NPCs may do the trick. NPCs besides the ones in the Pokemon Center and shop do nothing except give flavor text.
- Make it easier to engage wild pokemon (right click to start battle maybe?). Having to hit them with your pokeball is a tad annoying when the pokeball either misses or "bounces" off of grass or other things in the way. This also makes it a problem when you're riding on a pokemon and have to jump off to battle every time.
- Buff item space. Too much stuff to carry, like battle items, apricorns, extra gems in case Move Tutors appear while exploring, etc.
- Fix Quick ball exploit (fight, quick ball, run, repeat)
- PCs should have 100% spawn rate within Pokemon Centers. Not sure why this isn't already the case.
- Make silicon more useful. Currently only used to make Galactic armor and Porygon evolution items.
- Replace mobs with Pokemon in the Nether/the End. High-level Rock/Fire/Ghost types could populate the Nether, and Dark/Dragon/etc can populate the End.
- Remove Pokemon suffocation damage. I've seen Pokemon mobs die far too many times from spawning oddly, and it slightly takes away from the experience.
- Make berries plantable. I wouldn't suggest having them grow in the wild like Apricorns, because that would make finding them for the first time too easy. Gaining them from beating a boss and then being able to plant them would make them a neat reward.
- Replace diamond requirement for type Gem held-items recipes (Fire Gem, Water Gem, Bug Gem) with Crystal. I honestly doubt anyone would find spending 5-6 diamonds to make a one-use battle item to be worth the cost.
- Make it easier to send out a pokemon to ride on without having to press R. Possibly set a hotkey specifically for a designated "riding" pokemon in your party.
- Heal/revive pokemon without having to send them out physically. To my knowledge its impossible to use a revive on a pokemon without having to enter a battle using another of your pokemon and using a revive from the menu there.
- Redo boss pokemon movesets, i.e. boss Gengar only knowing Ghost-type moves and losing to a normal type. I killed one this way. You should also be able to run from these boss fights as well, in case you know you're going to lose, and said boss will regain all their health and PP when you do.
Will be adding suggestions as I come across them. I'm confident these are well thought out and implementable features, but let me know they're feasible or not.