So with Pixelmon, basically you're going to have to replace all the bukkit plugins with mods? Let's see
I'm not sure what Pixelmon has to offer other than Pokemon mobs so yeah.
-Money System
-Status Ailments? (poisened, sleeping, etc)
-NPCs?
-Pokedex Challenge (first 10 or w/e people to complete pokedex get a free mew? obviously when all 150 pokemon are made)
-Day/Night pokemon depending on minecraft world time
-Need pokemon with Surf to travel on water
-Need pokemon with HMs to continue through the map
-Remove jump ability?
-If a trainer kills a pokemon it dies forever?
-Difficult or very difficult like 1337 difficult challenges to reach legendaries
-One free masterball as always, 5$ irl for each masterball?
-Lose money when you lose battles
-Fly? Basically teleport only when you have a pokemon with HM(3)Fly
-I don't know how this can be implemented but whenever you defeat all 8 gyms, all 8 gyms get stronger each time up to a certain level. But only if you beat all 8 gyms. Ex. I can fight Brock again after defeating all 8 gyms and his onyx would be level 25, but some new player that never fought a gym can fight Brock and his Onyx is level 9.
Couple ideas, some are weird.