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You will miss out on one thing that's great about a link directory on your main site - a TON of extra pages.
GG loves huge, lumbering sites - just look at the SERPs. The more pages with related content, the better GG will love you. That's why I added my directory in with my main site and tried to put all the top categories in my sitemap.
I've also seen GG rank a lot of lists of links pages very high for certain types of searches. I wouldn't discount this either by using a different domain.
All that said, there's certainly nothing wrong with it, and I wouldn't personally have a problem with 3-way linking instead of reciprocal.
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