I'd really like to see more gene variations and interesting ways to get them (hybrid genes would be fun!)
Ideally it would be great if your nichelings could evolve into a completely different type of creature.
Examples:
Dragon - Lizard mouth, webbed wings, scaley body, lizard eyes.
Domestic - Floppy ears, wooly body, useless stub tail
Hooved - Hooved legs, mane, gazelle horns
Bird - Parrot mouth, extravagantly coloured feathers, bird legs.
Mythical - Unicorn horn, snake body 'back legs'
I wasn't really sure how to add this suggestion since it's all essentially one topic (more genes), but then I got carried away with examples, so I hope that's okay!