This is about the choices in games we don't even know we're making. Last night, as I browsed for some information on Monster Hunter 3 Ultimate I stumbled across something known as "Charm Tables". Now I won't bore you all with the minutia of how these work, but I will explain the basic premise.
Essentially when you create your character it's assigned a Charm Table (it depends on the time apparently), and it affects what items you can obtain in a rather significant manner. Once you're assigned one there's no way to change it, and since most things can't be traded in Monster Hunter (although this is for a good reason) you're permanently prevented from getting items outside your table. To add insult to injury there are a number of "cursed" tables which are not only significantly worse than the others but also prevent you from crafting certain high level equipment.
That's not the worst part though. The worst bit is that this is all done without the players knowledge. Not only do you not know the result of your choice, but you don't even know you're making a choice at all. It's worth noting that invisible mechanics are nothing new in gaming; there are many things that happen in the background that affect gameplay while the player remains blissfully unaware of how they function. However it's poor form to introduce a hidden mechanic that can drastically change ones playing experience for the entire game. Need that item? Too bad, you created your character at five minutes past two instead of quarter past three.
There's been numerous examples over the years, from Pokemon to Kingdom Hearts. In the latter the player is aware that they're making choices, but the consequences of those choices is obfuscated. While the choice of sword, shield, or wand is fairly obvious the player is given no idea that Wakka & Pals enigmatic pop quiz will dictate how they level up for the rest of the game. And if you plan on clearing all the endgame content slow levelling past 50 can really put a cramp on things.
Similarly Pokemon, like the Monster Hunter example these are choices being made without the players knowledge. The EV system is a set of largely invisible stats that are altered by which Pokemon you fight against, but unless you know about them already you don't even know you're affecting them at all. In this case the precise stats of your Pokemon will only make a difference on a competitive level. For casual play it's largely irrelevant.
Another offender is PSO, with its seemingly innocuous "Section IDs". Like the MH example this is something assigned when you create your character. Rather than the time of day it's based on your characters name. Similarly it affects what enemies drop and there are certain items exclusive to various IDs. Like MH it's a choice you don't know you're making, but at least you're informed of the results.
Still most of these aren't that bad. If you choose poorly in KH it just means that levelling up takes longer, EVs in Pokemon are repairable, and items can be traded in PSO. It can be disheartening though to invest a significant amount of time in a game only to find out you should have picked the handlebar moustache when creating your character. It's speculated that the Charm Tables weren't intended to be fixed as in previous MH games you got a new one every time you reloaded your game. Whether Capcom will correct this in a future patch or not remains to be seen.
Let me know what hidden choices or mechanics in games have infuriated you. In the meantime I have to go check that I'm not on a cursed table.