I think, from a game design perspective, his best bet for enhancing gameplay with minimal effort on his part, would be to make the bounty board mean something. He's removed the grungy trait so that Romy is useless: maybe he needs to bring that back but make it so that grungies can't breed so you don't accidentally spread it, instead.
Here's my thinking...
He could add a staging system to the bounty board so that early bounties reflect the available gene pool of the player.
The bounties could have a base orgasium reward defined by the difficulty of the request.
He could add additional rewards to higher tier bounties, such as population cap increases becoming available with Cassie, discounts with all orgasium based traders, add the opportunity to gain traits based on the highest value nephs with those traits when traded with people who don't trade with orgasium, and so on.
Another thing he could do is make the Alchemy Guild bounties into lending bounties, since they're only really after the fluids, which could level up and return the nephs after a few days, which means those bounties could be more demanding without the player needing to sacrifice some of their best nephs. That would present a good challenge.
(edit) Adding a mailbox in the style of Stardew Valley could add some good text based flavour and missions without too much effort as well. (/edit)
(edit2) Another idea would be to add an Intelligence stat, where wild nephs always have it at zero, and it only grows with player genes (or Blessed genes, if they become available). Then base the preferences system entirely on that stat, so low Intelligence nephs have few preferences and high Int ones have a lot (including the added value that comes with that). (/edit2)
Sorry, I sometimes drop tl;dr's, especially with my coffee.
