Armos Mazes - They're not challenging. They're tedious as hell.
OP'ed Enemy Spam - Overuse of Death Knights, Cracktoroks, Mirror Wizzrobes, Patra 3s, Fire Gleeoks, etc. No, just no. On a related note...
OP'ed Enemies - More whoever made those enemies in 1.90. This also includes Stalfos 3s in addition to the above. For 2.50, Leever and Goriya 3s. The former can hit you even when it burrows and is so fast you're guaranteed to get hit unless you have prior knowledge of its existence and Goriya 3 can easily hit you from anywhere in the room. On another note, Summoners if you make them summon high tier enemies.
"Touhou Rooms" - In Adam's Quest, these become WAY too common in the later levels. Again, these provide no challenge, just unfair mandatory damage. Mandatory damage = bad.
3 Heart Continues - Don't give me that crap of difficulty because having to run to the nearest Fairy Fountain every time I game over or spend the next 5 minutes grinding back to full hearts is NOT difficult.
Excessive Grinding - If you have to farm up 65,535 Rupees for an optional item that will break the game, fine. But if you have to gather 500 Rupees just to buy an item needed to get into level 1, count me OUT.
Cane of Byrna - It drains magic WAY too fast. Even if it's set to use no magic at all, for me at least, I find the cane actually gets me hurt MORE than not using it.
Magic Wallet - Infinite Rupees? Really? If it actually worked as intended (unless it was fixed in 2.50 Final), it's still awesome but impractical since by the time you would realistically get it, it's useless.
Magic Key - Another awesome but impractical item. In both the 1st and 2nd quests, you don't need it if you don't unlock every single door. Now granted, I know a lot of custom quests actually give it some use, but still.
Shops that sell keys - So instead of doing the dungeon, I can just grind up Rupees and take the easy way out?
4-Way Ladder - Just seems like a gimmick if anything. Plus using this with diagonal movement is next to impossible >_<.