Tiers have nothing to do with Game Freak, they're the result of an independent group with their own measurement system.
The idea is that after eliminating the obvious "ubers" like Mewtwo and Rayquaza, the remaining field is called OU in which players can use anything else. This means you can still use Pokemon that are designated UU, RU etc. in an OU battle, they're just not the most common choices there.
In order for a Pokemon to actually be designated as OU, and thereby forbidden from being used in lower tiers, the calculation they use is "Consider the concept of 'a full day's play' to mean 20 battles per day. If a Pokemon is used on enough teams within a tier that you have at least a 50% chance of encountering it once over the course of a full day's play, then it gets tagged with that usage tier, otherwise it's allowed to slip into a lower tier." So the cutoff is exactly 1 - 0.50.05, which works out to about 0.034: if a Pokemon is used in less than 3.4% of OU teams, then it's allowed to fall to UU; if it's allowed in UU but used less than 3.4% of the time there, then it falls to RU, and so on. Generally, people won't use a Pokemon very often if it's not very good against that tier's main competition, so this mechanism should neatly sort everything out into a variety of strata in rough correspondence to overall power level.
There are a couple more complicated factors to finish off: the usage stats are generally only calibrated once every three months, so usage trends in certain months plays a bigger role than other months. Additionally, lower tiers are allowed to maintain their own explicit banlists beyond what comes and goes through the natural tiering system. So for example, if you have a Pokemon that isn't used enough to meet the usage threshold in OU, but it's deemed too strong to deal with in UU, it can get tagged with the designation "UUBL". Functionally there's not a lot of difference between being UUBL and being OU: both designations mean it can be used in OU but not in anything lower. Still, they remain as separate designations for the ease of maintaining future tier shifts.