Apologies if any these have been suggested already, I read through the thread and didn't spot them.
First one's a doozy:
Rework stat system
Most stats should be listed as raw values, ie combat, sex skills etc. Having them as percentages, capping out at 100 for all stats on all girls, is kinda boring.
Each girl should have a 'natural' value for each stat. This might be hidden.
Percentage changes (from experience, training, some items and so on) should add points toward this natural value, but never above.
ie current Bestiality value 20, natural value 50, adding 50% -> new value 35.
Static changes would simply be added after percentage gains/losses. Same example, add 50 raw instead of % -> 70
This way each girl would be useful for some jobs and garbage for others, regardless of training, but traits and items would retain their value, as they could grant percentage or raw as desired.
This leads on to my second suggestion:
Job permissions specific per girl
Basically move the 'allowed acts' section from the brothel management screen to the girls'. This way you tell individual girls to perform specific acts, rather than have all your girls in each brothel do the same things. You could also avoid acts which girls are currently inexperienced with to prevent them getting hurt, while training them to a level where they'd be better at it.
And this leads to my third (and favourite):
The permissions tickbox box

Basically that. It bothers me that the current BDSM option assumes the girl is submissive.
Again, apologies for any reheated concepts.
Also, best wishes to the dev team.