Pidgeot: Make it happen, GOG, or at least be honest about the *real* reason (because it sure as hell can't be "no VNs allowed").
Well, it's diplomacy. It's often not in a company's best interests to be fully transparent on all the real reasons for rejection (sometimes there are even legal liabilities involved in revealing this information). From what I've read about GOG's rejection practices, however, does leave a lot to be desired in terms of developer relations. Reading between the lines, I would imagine the true reasons for rejection are (in order of importance):
1. It's central focus is on sexual themes and eroticism, which is a highly controversial / taboo subject matter. The uncensored version has explicit artwork which some find to be more shocking than seeing artwork of someone's brains splattered all over the ground, and that can affect brand acceptance severely (in business terms).
2. It is a "casual" match-3 puzzle game. Do you see any other match-3 games on GOG? They don't even have a puzzle category, and GOG has historically selected titles that catered more to the crowd that typically shuns "casual" games.
3. At the time of its submission, I don't think it was very well-known and I believe GOG prefers to select games with a strong following / hype prior to release which increases the per-title profit potential of each game they allow into their catalog. Now that the game is demonstrably popular and has a following, this point probably no longer stands if they game were to be resubmitted for consideration today.
4. It has some design influence from VN, although this seems like less of a real reason since Long Live the Queen and Hatoful Boyfriend are actual VN and are available for sale on this site.