Weirdly I only just now remembered a big one that was supposed to go into the OP, but... despite being the inspiration for the thread somehow got utterly forgotten when it came to write it up.
Build Substituition Meta Rules*
This is when the game designer puts in methods of making alternative 'builds' for characters, usually to overcome some deficiency in his design, as a patch, and is closely related to the phenomenon of keeping PCs weak and incompetent (the zero to hero, where Zero is often roughly equivalent to a twelve year old child in terms of general competence). The first time I ever noticed it, and a decent example to explain what I mean, was in Brave New World, where they introduced a new Martial Art using the 'Spirit' stat to make 'battle nuns' more competent fighters. I vaguely recall that by the end of the game line you could have a Martial Art based on any of your stats, so you could have a nerdy martial artist who could beat Bruce Lee by punching him with his brain-thoughts, or maybe I only imagined that because of the implications of the addition of the Two-Inch Prayer Fist.
I've noticed that the Mutant Year Zero game line does this an AWFUL lot. There are only four attributes and twelve common skills, but there are about twenty talents between teh books that let you change which attribute covers which skill (usually for the Career skills, but still...). So, for example, you can have an investigator who solves crimes with his 'social' stat instead of his intelligence stat, meaning he can put together and spot clues even if he has a room temperature IQ. This is especially hilarious as the MYZ's dice pools are generally small enough and the cost of a talent is the same as a an additional point in a skill that it should almost never be viable to take these talents unless you really did make a genuine Moron as an Investigator. So the real reason is, so far as I can determine, to take advantage of the already incredibly Meta 'Push' rules.
To me these sorts rules represent a point in the game's design phase where the designer should have asked himself 'why does a battle nun 'not work' unless she can stack a combat skill under her faith stat? Why would any player need a special talent to make a social/intuitive detective viable over a smart detective (In this case: Because of the need to "Push" rolls, and with four Houses each given a single Attribute they can Push, without this talent only members of House (For Elysium, different Year Zero games divide up the push stats differently) Kilgore would ever be viable detectives!). Its a immersion breaking patch rather than a proper fix. The BNW model (alternate skills) is just nonsense that damages immersion, in the MYZ model, you actually wind up trading rare character resources (talents, which cost XP and represent a major part of your character's growth) to simply' tread water' in trying to make a non-optimal character (which should totally not be non-optimal... Recall: the purpose here isn't to make a Columbo who solves most of his crimes by talking his suspects into incriminating themselves (a bad description of Columbo, I know...) but to patch over the fact that only Investigators from House Kilgore (who get free Pushes for Wits checks), would actually be competent in the High-Wiff MYZ ruleset. SInce in real life people don't work that way we make reality break so people can stack more skills onto their 'free push' stat via talents so they can acheive basic competence.
I'm not trying to pick on Brave New World (not that I'm worried about rabid fanboys for a more or less dead game) or the Year Zero engine games. I've seen this elsewhere, but they were the examples most ready to mind for me, for reasons I think I explained well enough above.
*I honestly have no idea what to call this, so forgive the clunky name, eh?