Totally agree.I agree with you and most VNs here are among: do I go first for story a and then b, do I want either LI A, B or both - so overall either choice that omit some story elements already in the game, minor things or flavors.
Having "real" "big" choice in a game leads to either having only a few choice (eg. choices going for endings 1, 2, 3) or it makes the game a "nightmare" or very short.
As Harem Hotel is already a big game, I doubt that anything other than minor or flavors choice will be in it, simple cause otherwise the scope and size of the game would be much much bigger.
Eg. for the whole slave no slave, that at least are 2 big choice and could, if wanted end with a lot of difference scene and I guess 50% more game size if both paths were equal. Adding "good" slaver, "bad" slave and on the other site "true" freedom fighter and "turncoat" freedom fighter, with a lot of choice, unique paths, paths crossing, unique scene and reactions from all the NPC, would make the game big and bigger.
And although such a game is interesting and is more realistic than "choice a for path a, choice b for path b" it is often so, that you invest a lot of resource for a path only a handful of people will see at the end of the day (because it is to specific to a route...).
Therefore, I doubt that Harem Hotel will include more path than it already has.
It's a matter of resources.
It would be hard to do it for practical reasons.
Probably it won't be done.