What's the difference between these phrasal verbs? Would you say "organization shake up", "organization shape up", either depending on context and desired meaning or neither? How about "documentation" in place of "organization"?
"Shake up" implies that things are getting changed around, while "shape up" implies that something is bad and should be changed. So if someone says "organization shake up," they're simply stating that for whatever reason something is getting changed around, whereas an "organization shape up" means that something needs to be improved.
The phrases aren't used in the same way because one is transitive and the other is intransitive.
To shake something up means to disturb or rearrange it, often with an intent to improve. It is transitive; "I will shake up this football team."
To shape up means to improve or become more fit for purpose. It is intransitive; "Shape up, man!"
I wouldn't normally say "organization shape up" at all.