Shadowyard ships are bright and cartoony blue and green mixed with ugly browns, and the portraits are animesque. The art style is radically different from the base game, and do not mix well. This alone is a reason for me not to include Shadowyard if I feel like playing with faction mods. Another reason is few of the weapons are noticeably more powerful than standard (though not to the extent of Templars or Neutrino) or at least remove the weaknesses energy mounts have. The mod is not bad per se, it is fairly good, but the art style makes it feel belong to another game, not Starsector.
@ Nanao-kun: It is not because they are organic. Some Blackrock ships have an organic look (Imaginos and Morpheus, at least) and I am fine with them.
P.S. Shadowyards is something to include if there are not enough other faction mods available to use, like right after a major version update. I need to give credit to MShadowy for maintaining his mod, despite my reservations on it.
P.P.S. Shadowyards is like the commercial "South Pole, Dora the Explorer: It's What You Do - GEICO", where Shadowyards is Dora.