PokéBase - Pokémon Q&A
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Search it up yourself!!! (Why do I have to keep saying this......)
Totally unrelated, but there's an OM (Other Metagame) called XY FU. They allow any Pokémon that are 3.406% or lower in the usage stats to be used. However, Regice and Vigoroth have been banned.
More info here: http://www.smogon.com/forums/threads/xy-fu-regice-and-vigoroth-banned.3519286/

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Best answer

PU stands for nothing.

It is a pun on the phrase "Pee Yew!", meaning something stinks (kind of like the Pokemon in PU!)

Source:

Welcome to the FU Metagame for X&Y! Because PU wasn't enough, FU allows all the PU Pokemon that are 3.406% or lower in the 1630 usage stats to be used. Surprisingly, there are quite a lot of decent Pokemon available to use. And much like PU, FU is not an acronym for anything.

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This Smogon forum post tells what PU is Click Here for Info!PU is basically is a tier below NU and it stands for Partially used. It gives weaker Pokemon a chance to shine.

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Your source doesn't match with your answer.
" For those of you who don't know, PU allows all the NU Pokemon that are 3.406% or lower in the 1630 usage stats to be used. "
Which means those NU pokemon that are not used enough are considered PU pokemon. That puts PU below NU.
Oops crossed my Mind i forgot xD