HM01 Cut: Can cut down the little pixelmon tree that blocks your path but no other tree. This would prevent players from destroying other bits of the world and allow the need of cut. It would also be cool if that tree respawned after a min or so.
HM02 Fly: As much as I love flying on the back of pokemon, with a project like this isn't quite fly friendly. You get high enough or far enough you either lose the map or you see all the ugly edges. It'd be nice to have nameable "fly" blocks. That you can place, and once you have discovered them you use fly opens up a menu and send you to that location.
HM03 Surf: You go swimming while not ridding a pokemon hurts you health, or teleports you back on to the land. And pokemon can't go below the water.
HM04 Strength: Strength boulders (effected by gravity, so can work as both new and old) that when strength is in play you can right click and it'll push the boulder in the direction your facing. Also reset after some time.
HM05: Defog when used does the /weather clear command
HM06: Rock Smash, basically the same thing as cut, a boulder the player can't jump over, that rock smash can only destroy that. Resets after a min or so.
HM07 Waterfall: Not sure how this would work, maybe special waterfall blocks you can only go up when using waterfall.
HM08 Rock Climb: Similar to water fall special blocks you can only climb when using rock climb.
HM09 Whirlpool: Special block that sucks items and entities into it, as well as removing the blocks in a upside down pyrimid shape, so it all collapses onto that block. When whirlpool is used is close proximety it removes the block which respawns a minute later.
HM10 Dive: If player goes underwater without dive suffers damage.