Thanks a lot for the thoughtful comments. To address your feedback, the idea of making Thim available as a partner has cropped up from time to time, but I don't think I'm the right person to write male on male erotic scenes. I've read some male/male romance novels in the past and it just doesn't have that spark for me, so I don't think I'd do a relationship like that justice. Another problem is that it creates yet another story branch for me to develop and the game already is quite expansive for me to keep together.
The same goes for Vess in the brig actually. She'll be freed from the brig eventually, but developing a romantic path post-brig is going to be a lot of extra work to make it believable. With everything else going on (the single relationships and various harem configurations), that's a strand too many I'm afraid.
I'm glad to hear that you find the game more interesting when playing with a full relationship roster. Ultimately these games are about fulfillment, so the game certainly won't punish you went you go for all of the available love interests.