Balance out the mutations.
For example, a mutation provides a negative AND a positive effect. So you get a mutation that makes your tame have more health, but also deals less damage, or your tame has more movement speed but has reduces stamina.
There could also be weirder, and much rarer mutations, like....
1. Reduced fall damage
2. Increased fire, electric, or poison resistance.
3. Tough hide to Increase physical resistance
4. Sharper teeth [ (x)% chance to inflict bleed over (x)seconds]
Just a few examples, but it would be much more complex a