... the adults from the children is the obvious way. You could also get more creative, like ... the heroes from the zeroes or somesuch. Doesn't seem like a particularly sticky problem to me?

I would go with "...separate the experts from the rookies."

Jedi from the Padawans?

The weak from the strong...

@DanBron I would contend that "adults" and "children" do not have the same semantic connotation in your proposed phrase as "men" and "children" do in the original.

I recommend "separate the newts from the efts."

Considering how macho the original phrase is, a gender-neutral version wouldn't be the same.

You could avoid the use of the cliché altogether.

@AbraCadaver As cringeworthy as using that phrase is to some, it is, IMO, not a bad replacement. It's topical and is fitting of the meaning. I would also believe that more people would understand that comparison than would wheat to chaff.

"Has anyone found a (...) [gender-neutral version] of this expression?

Idioms are product of a culture. The culture that generated "separate the men from the boys" is a culture that does not blend well with degendering. It suggests that there is a coming of age process that is uniquely male, or so different among males than among females that it deserves separate language. You can convey the distinction between those who can and those who can't in a variety of ways. Answers and other comments have given lots of help here. But all of them lack the flavor of the original. The flavor of the original is not genderless.

wheat from the chaff

@AndrewGrimm: Challenge accepted! See my answer.

I always liked "..is when you get to sit at the grown-ups table.'

"..separates the Transformers from the Go-bots."

For what it's worth, I would avoid this phrasing and any variants on it just on the basis that it will remind anyone familiar with it about a juvenile and distasteful joke about pederasty...

"Separate the masters from the bachelors..." ?

This is indeed a gendered expression, but don't forget it's also ageist (it evokes discrimination based on age). Perhaps you'll want to avoid ageism as well?

"phrase that doesn't show disrespect for the folks who are not up to doing the difficult proofs" ==> isn't that exactly what that phrase is designed to call out, those who are not up to doing the difficult proofs?

@WalterMitty : Very good, +1. The whole point of using an idiom like this is -- IT'S AN IDIOM. It isn't meant to be taken literally. If you think you are offending boys by using the idiom, then you're pretty dim in my book.