Goodness I am sure I have quite a bit of these.
In Dwarf Fortress there is an easter egg where someone will fall down a well. Now this is all said and good except this chance only increases with the number of dwarves around it. You can have a well falling epidemic rather easily!
In Creatures 3 your ship has several ecologies. Except that it is relatively easy (by just doing nothing) to have entire species die until all your habitats are boring. It took a Fan made creature (Gaia) to fix this.
Hmm Ill have to think harder... hmmm...
Ohh In Suikeoden 2 there is a series of 5 secret characters (flying Squirls) 4 of the 5 (though if you miss the first squirl you have to try again) require PURE LUCK and psychic powers in order to get. Honestly there is nothing that makes me want to destroy the world more then to try to collect all the flying squirls.
-The exact requirement is your supposed to travel specific roads between two places with no one in your party. Ive done these for hours and I never got all the squirls. Too bad too because I like Mikumiku.
In Suikeoden 3 you are more then capable of killing your entire party with spells. Worst yet one of your major characters learns a mass attack spell rather early which only serves to kill you and your party the first time you use it. Near the end of the game however characters have such large movement radiuses that they will almost never be hit making the mechanic superfluous.
-Near the end of the game you have to fight 4 bosses with 4 different sets of characters. ALL of them need to be almost maxed out in order to win. What was that? you had a main party for the whole game and havn't trained anyone else? well I hope you have a save point.
Scale in Dragon Age Origins. The issue with the game is that everyone levels with you (even the enemies) but the issue is that they NEVER change the enemies up. So what ends up happening is it entirely kills your sense of scale as even the wolves you fought earlier can easily dismember you. It just makes you feel like a weakling FOREVER!
-This is of course ignoring the equally horrific "I like you" mechanics. Watch as not being a total jerk who only cares about himself and who doesn't have the forsight of a cat causes many of your most important allies to suddenly hate you!
--OHH and let us not forget how expencive many items are in the shop. Some items are SOO expencive that you can litterally NEVER have collected enough money to afford them. Luckly there is an exploit for cash.
Radiata Stories: HOLY GOODNESS! Look Square enix your not getting it. There is NO point to collecting a ton of characters if the vast majority of them are going to be totally useless. Worse yet is your Newgame+ feature is next to useless.
-To explain in Radiata stories you can get almost every character you see on your team. However you cannot change their equipment and they never get better attacks. So if a character wasn't good before you used them. He/she isn't good after you use them.
Dance Dance Revolution (a few of them): Alright I can understand making some songs difficult to unlock, but is there some sort of malicious humor in making some of these songs require either endless flawless input on several songs (like
or that require excellence in some of the most infuriatingly difficult songs in the game? I will NEVER have the skill to unlock them and I assume most other people cannot as well. Songs are important features (worse yet I heard the song too, it is good!)