As far as the characters go, I think their behavior is consistent, as they are so thoroughly evil, that some hypocrisy about loyalty is just the tip of the iceberg. The typical harem game protagonist gets some super power early in the game and his first thought is: "Great, how can I use this to rape my mother?". In most harem games the protagonists see the women as possession rather than as partners and essentially he doesn't want his slaves to serve other masters. Personally I find it more inconsitent, when such a protagonist suddenly, between enslaving all female family members, co-workers and neighbors, discovers his romantic nature or acts in virtuous way.
Incest Story was certainly inconsistent in that way, as the protagonist, despite fucking anything that has a vagina is somehow described as having a romantic relationship with his mother. So in general for a harem game to be plausible in itself, the protagonist has to be a complete jerk and using some means of blackmail or coercion. Otherwise the chance to get a mother to lick her daughters pussy, while her son fucks her, is quite low.
I think a polyamorous game would be fairly different from a harem game, though I'm not sure if a lot of people would play it. I personally would only play a lesbian polyamorous game, but not a straight or bi one. In general I think a polyamorous game - regardless of orientation - would work best with a "multiple protagonist angle", so it doesn't have the smell of NTR on it. It could be something like the Sims with a large household and disabled jealousy settings.
