Still kind of stuck on the ideas front; that list of 100 kinda took up a year's worth of material. So instead I present a couple of smaller ideas, which can be shoehorned uncomfortably into a generic game model of your choice.
Palette Swapper
Since time immemorial (well, the NES and early home computers, but that's about as far back as you can go in this case) RPGs have used the cheap-as-heck method of palette swapping to create new enemy sprites out of existing enemy sprites. The reason being, of course, that enemy sprites take up a considerable amount of the sprite artists' time and short-cuts are necessary to meet deadlines. Since we've come along a ways and now have more sophisticated ways of editing a second similar enemy's appearance (such as adding a couple of horns or something), we can warmly homage this ancient practice with this new feature.
In this scenario your odd, occasionally fourth-wall breaking additional secret character learns an attack where they can change the palette set of an enemy they're fighting. What this does is entirely dependant on the enemy and the palette colour/scheme you give it. If you have the "Red" palette attack, for instance, in most cases the enemy will become a fire-based enemy. It'll also occasionally turn them into a much stronger/weaker variant of that enemy class, which will either increase the difficulty for a better reward or make the battle slightly easier in exchange for a lesser reward respectively. A sneaky design team might even hide special, powerful items by making sure an enemy drops them only when they've been turned a specific colour that boosts their stats. In fact, a lot of the earlier dungeons may suddenly become home to many potentially devastating enemies and the inevitable fantastic rewards that come from accepting such a challenge. Old-school RPG fans (in fact, they don't even have to be all that old-school because games still actually do this) will appreciate the meta reference too.
Clone Spell
A lot of games have tinkered with the idea of a clone spell or an effigy of some sort, in which you'll have something that will take damage for you or distract the enemy while you're busy elsewhere. In this idea, you have the ability to create shades of yourself that can only do one of the many things you're able to do. So in a dungeon, you're able to use a shade that can open chests but nothing else - no jumping, no fighting and no disabling traps. But you also have a shade each for all those things too. You might also have a few dummy shades that can simply be fodder for whatever trouble you might face. They can only be used once per dungeon, and it's up to the player's discretion to use them at the appropriate moment.
The twist is that these shades can be powered up if you use them right. If you use the chest-opener as an enemy distraction since you're pretty confident you're able to open all the chests in this dungeon without its help, it won't earn any experience as it is not fulfilling the role it was meant to fill. Levelling your specialist shades will allow them to surpass you in their given speciality. A chest-opener in this case will find better treasure or more money than you would have normally. A fighting shade will be stronger than you and perfect for bosses or otherwise particularly tough bouts. Choosing to squander or ignore even the most mundane of shade abilities (like a shade that can only jump up a small cliff) may have unexpected consequences later on (in the example given, that shade will eventually be able to jump a huge, impassable cliff in a later dungeon and activate a footplate that will lower a ladder).
Obviously, we can't penalize players too strongly for choosing not to do something at an earlier, now-missed stage of the game, but we can take nice rewards away from them for not playing ball. Because we're asses like that.
Okay, so, maybe there won't be a cop-out post next week. No promises though.
