I'm doing some serious bee work, and while I really like the fact that Gendustry makes it all a heap easier (I never really progressed too far with bees in the past because the RNG just got too annoying when trying to breed).
That said, Gendustry is just OP. If you want a bee breed, you can basically get your hands on the relevant Princess and Drone, chuck them in the Mutatron, and bingo, better bee breed. So these are just my thoughts about how things could be improved to make it a fairer game.
First of all, have a couple of tiers of Mutagen, the raw Mutagen will only give a 40%-50% chance of getting a new breed of bee, but you can purify it up to 3 times which will give you a 90% chance of a better bee breed. Purification takes a metric ton of power and time and will also reduce the amount of Mutagen, maybe something like 25% reduction. By taking time and power would mean that it makes it less of an option for early game as it takes time to be able to produce, and the power requirements require a good power generation system. By having a cap on the chance of getting a better bee, then your not likely to just blindly chuck your only princess and drone in there as there is always a risk that they'll end up as a cross breed.
Maybe another option is for the process to fail (maybe again dependant on the quality of Mutagen), so that it just fails and you get nothing back.
As I said, this makes bees a much easier option, but right now, the hardest thing with bees is draw up the list of breeds that I need to work my way through, or because of my preference on working with bees, is to wait for a new Princess to be bred.