5. The Everstone
Evolution is one of the most integral parts of the pokémon games. With a few simple levels, your pokémon will transform from a puny pile of crap to a fire breathing beast of death. Unless, of course, it's equipped with an Everstone: An item that allows your pokémon to level without the strain of becoming too useful.
The Everstone made its first appearance in Pokémon Gold and Silver as the second prize in the bug catching contest (and considering first prize was a Sun Stone, you should probably work a bit harder next time). Stopping pokemon from evolving can allow it to level faster and learn moves earlier, so the Everstone seems useful on the surface. However, pressing "B" does the exact same thing. And you don't have to be runner-up in some stupid bug contest. Then again, you wouldn't want to strain your thumb reaching for the "B" button.
4. The VS Recorder
Not to be confused with the VS Seeker, the VS Recorder is a device that allows you to record your battles. What's the in-game benefit of it? There isn't one. You get no experience, no cash, no items, NOTHING. The VS Recorder is used exclusively for players to smugly show off their mad skills as a pokémon trainer. Essentially, all they're doing is showing their lame battle to an audience that will undoubtedly just find fault in their technique. Beats going outside, I guess.
3. The Pokégear Radio
Pokémon Gold and Silver offered a range of changes in gameplay from Red and Blue. They added a day and night system (new pokémon would be seen at different times of the day), there was a phone that allowed you to have rematches with former opponents and then finally, there was the radio.
And what did the radio do? Not a lot. For the most part, it was just scrolling text backed by a soundtrack only slightly different from the regular gameplay music. There was also a Pokéflute channel that, get this, played the music of the Pokéflute! The only real use to this was to wake up a Snorlax (the apparently narcoleptic pokémon) that is rudely blocking your path. In some ways it was a nice idea, but all it really did was allow you some hours to sit watching characters having a conversation. If you want that, you may as well go read fan fiction.
2. Useless HMs
Your pokémon only have four move slots. Do we really have to use one up to make room for an HM that only comes in handy for one part of the game? The only real use of HMs is to stagger your progress between towns. If it wasn't for that pesky little tree, you would have been in Vermillion City ages ago! For each of these wonderful little obstacles, you have to find a specific HM and then find a pokémon that can use it (most can't). Since most of them are useless in battle but necessary otherwise, most people end up having a pokémon in their party just used for its HMs. An HM Bitch if you will. A total waste of party space.
1. The Masterball
This one's a bit controversial. A ball that catches any pokémon without failure is indeed incredibly useful. But the concept of Pokémon is to travel the world fighting, defeating and catching pokémon. The inclusion of the masterball completely cheapens the entire concept.
Let me put this into perspective for you. Your character is a young hero who has left his mother behind and embarked on a grand adventure. Criminal organizations have fallen under his might. Grown men have wept at his feet. Finally, you face your greatest foe: A Pokémon of legend. A monster that was said to have created the very ground you stand on, that has flooded cities and annihilated everything in its path. You are the only person that can face this beast. The story of this battle will be passed down through generations. And what do you do? You throw a fucking masterball! Through no challenge or skill, you have managed to catch the greatest of all the Pokémon. Any victory you have now will be a hollow one, devoid of meaning. I hope you're happy.