But Nobles wouldn't "stay" nobles. They would always degenerate for me. The princess would become cultivated or common.
Bee's don't just degenerate. You have to have a basic understanding of genetics to understand what's happening. You also ABSOLUTELY need the beealyzer. You really don't need any of the machines to get industrious and imperial bees, it just makes getting traits like "fast" and "nocturnal" into those bees easier.
You ahve to keep in mind that if you breed two bees that don't have the same 4 race traits in them (2 for the princess and two for the drone) that there's a chance that the resulting princess has any combination of the race genes. The same goes for the drones that you get out of it.
So a simple example: let's say you breed a "cultivated-cultivated" princess with a "common-common" drone. There's a number of things that can happen. First of all, there could be no mutation at all. This will result in the bees you get out of it (1 princess and 2-4 drones) to either be a "cultivated-cultivated" (pure cultivated), "cultivated-common" (cultivated-common hybrid), "common-cultivated" (common-cultivated hybrid) or "common-common" (pure common) princess/drone. Basically for each of those combinations you have a 25% chance. And every resulting bee is random.
What can also happen because a cultivated princess + common drone can result in a mutation is that you get a mutation in the genome. This means that one of the "race" genomes in the resulting drones be either "noble" or "diligent".
So let's say that the result is:
1 princess: "common-noble"
1 drone: "common-noble"
1 drone: "cultivated-common"
Unless you analyse the princess and drones you dont' see the exact traits. If you now breed the princess (common-noble) together with the drone (common-noble) you have a a 50% chance that the resulting princess will have atleast 1 "noble" trait and about 25% (IIRC) that it's a "noble-noble" princess. The same for the resulting drones.
So basically for every race of bee you first try to cause the mutation, and then you purify that strain be selecting the drones that give the highest chance of the resulting princess and drones to be "pure" (noble-noble). Since if you breed with 2 pure bees (a noble-noble princess and a noble-noble drone) you will ALWAYS get a pure bee back. Bees never spontaniously degenerate, you were simply breeding hybrids.
Make sure you understand how this works. If you don't you'll simply be wasting your time. The first few upgrades (mundane > common > cultivated) you can do by just guessing based on the bee color but after that there will be so many hybrids that you'll slow down too much.