yeah even tho im not a fan of threesomes it feels a little weird a shitty to exclude only Main girls from them when it's a harem game. I wouldn't say no to Eliza and Amelia for example even tho I prefer them alone
Personally, I love threesomes (and more). But character or story reasons asides, creating group sex scenes with optional harem games like this where you can pick and choose individually can be a nightmare due to all the possible combinations. As an example, one other game I play recently had a group sex scene with up to 4 of the main LIs, but it had variants of the scene depending on which LIs you had "on" path. The result was that the dev had to make 11 different versions of the scene, with altered renders and script for each version.
I suspect that's one reason there might not be as many in Nephilim. Threesome are much fewer variations, but still will mean that people that aren't going full harem might miss content and not even know it.