Why isn't "Agricola: All Creatures Big and Small" called "Agricola: All Creatures Great and Small"?
I am almost certain this is a UK / US difference. Specifically, I believe it was named this way because of a marketing decision by the US publisher.

Research:

Although Agricola's creator is Uwe Rosenberg: "a German game designer", the main publisher is Mayfair Games:
"an American publisher of board, card, and roleplaying games"

As you mentioned "All Creatures Great and Small" is a well known UK book/tv series.
This page, shows release titles in different countries. Each language's word for "Great" (Spanish: grandes, Italian: grandi, Dutch: groot, Polish: duze, Russian: большие) all translate to "big" or "large". Even though that is one of the definitions of great, they don't immediately translate to "great". "Big" is a simpler translation that cuts straight to it's meaning.

Why is that simple direct translation relevant? Because that's one common difference between UK and US English. Americans tend to simplify English (some might prefer to say "dumb-down" haha). Check out this page for US/UK spelling comparison, where in every example the US version is just simpler. 

I would bet that if the TV series, "All Creatures Great and Small", were remade in the US, that they would change "great" to "big", just like they did with this movie, "All Creatures Big and Small".

If we take a look at that movie's release titles in other countries, the title chosen for UK is "Two by Two". Perhaps they knew the phrase wouldn't sound right in the British ear, and "All Creatures Great and Small" was an already well-known title there.

Moving on, let's find the phrase in a dictionary.
The only one I could find that accepted the phrase is OxfordDictionaries.com. Both phrases using "great" or "big" bring up only the phrase "All Creatures Great and Small." So I would call that the proper or truer phrase. Found on this page.

Did Americans change other phrases using the word "great"? Dictionary Time!
Not only other phrases but if we look at some of the example sentences given for the definitions in this Oxford UK dictionary, a few don't sit right in my American ear.

UK Dictionary: "I was a great fan of Hank's" --- US preference: "I was a big fan of Hank's"

UK Dictionary: "You great oaf!" -- US preference: "You big oaf!"

UK Dictionary: "My father was a great one for buying gadgets" meaning an enthusiast (In US, this sounds like he was skilled at buying gadgets at good prices)
-- US preference: "My father was a big one for buying gadgets" (communicates more of a liking and enthusiasm for it, in the US)

UK Dictionary: "to a great extent" -- US preference: "to a large extent"

(Note that the "US preference" is my personal American ear's preference, so I'm curious if other Americans disagree with any of those.)

Wish I could find more definitive proof, but hopefully this is enough evidence to at least satisfy your curiosity, in case we don't hear back from the game's creator, Uwe Rosenberg.