In all grassier biomes, tall grass should spawn in patches, which slow you down noticeably, but not as badly as soul sand. in the middle of these patches could be a reward, which would create motivation to enter them.
A new type of stone called burrowed stone, would help elivate the issue of pixelmon not spawning underground, as they can spawn if you step on this type of stone. Also imagine the trolling.
Mountains could have snowier snow that has the same effect.
Other biomes could have patches of different coloured sand.
And whirlpools could be added to the oceans and other bodies of water.