While I try my best to keep everything as close to the games as possible, sometimes I just can't. Here's a list of major deviations from the games:

• Strength puzzles are not implemented in any form yet. Minecraft just doesn't have anything close to them
• The Kanto Safari Zone could not nearly fit into the world map in its actual location, so each sub-zone is in the blank areas between routes. Command block teleporters ensure it still acts like one complete area
• The Dragon's Den in Blackthorn City is flipped upside-down so the entrances line up
• The text of many signs is shortened or abbreviated to make it fit
• Johto is mapped as it appears in Gold/Silver, but includes the Battle Tower from Crystal and Routes 47, 48, and the Safari Zone from HeartGold/SoulSilver
• I Had to make a few two-block-thick houses one block thicker to fit teleporter pressure plates
• Due to the perspective of the maps, multi-layered areas, like mountains, don't translate to 3D perfectly. This is because in the games, a cliff edge takes up one square, but obviously it doesn't in Minecraft, so I used gravel for cliff edges. This gravel should not be walked over, since you can't walk over cliffs in the games
• Sootopolis City is in a crater, not on a volcano/mountain, because it's too large to fit on top of a mountain
• Interstitial areas (the empty areas between routes that you never see in-game) are generally filled in with thick forests
• The Desert Resort in Unova is far too large to actually fit on the map. It would extend west of Nimbasa City and block the bridge there, so the long route leading up to it is shortened considerably
• Spear Pillar in Sinnoh is a little smaller than in the game due to size constraints