Nonsensical Pokemon Decisions
There are many poor game design decisions made by gamefreak when creating the pokemon games, but this list is not about them. This is about the ones that don't make sense in any way. Things that cannot be explained by lack of foresight or incompetence, where it would have been easier and more beneficial to do something different, and this fact is obvious to even the most layman of observers. The most nonsensical decisons of them all.
Pokeathlon Purchaces
In pokemon HeartGold and SoulSilver there's a set of minigames called the Pokeathlon, where you control your pokemon to compete to win points. These points can then be exchanged for items. But gamefreak decided to make it so regardless of how many points you've racked up, you can only buy one of each item type per day. This is not a feature in any other store in the game.
Arbitrary Transfer Limits
When transferring pokemon from Gen 3 to 4 using the pal park, you must transfer 6 pokemon, and you can only do it once every 24 hours. Fortunately the time limit was removed in HeartGold and SoulSilver.
The Arceus Event
In the Gen4 sinnoh games there is an event where you can encounter Arceus. After obtaining the Azure Flute you go to Spear Pillar where you are prompted to use it, then a glass stairway appears and there Arceus stands waiting for battle. However, this event was never released. In an interview much later on Junichi Masuda gave reasoning that it was "too confusing" to use, which of course makes no sense.
Challenge Mode
Difficulty settings were something fans had been asking for in pokemon games for a long time, and in Black and White 2 gamefreak finally delivered. There are two alternative difficulty modes you can play the game in: Easy Mode and Challenge Mode. But there's a catch, you have to play through the entire game first, then delete your save file in order to be able to access them. Yes to access Easy Mode, one must first complete Normal Mode. But that wasn't enough for gamefreak, they also made these modes version exclusives, so you need a friend with the opposite version to access both Easy and Challenge Mode.