I don't get the fun side of blundering through someone's pre-programmed series of "discoveries". Specifically I'm referring to Thaumcraft and Forestry. I've been messing around with bees for a couple of days now and I have no idea what I'm supposed to be doing. I just want some Royal Jelly so I can make Dispersion Capsules. So far I've got one Cultivated princess and a three Common princesses and a bunch that keep alternating between different species each generation depending on what drone I breed them with. It's been a frustrating waste of time. I looked up all the Thaumcraft stuff so that I could try to navigate my way through the discovery, and I don't feel like I missed out on the fun of discovering it myself. Having tried to fo bees by the discovery route, I think I was right to read up on "spoilers", and now I'm going to do the same for bees.
Phil you've pretty much summed up my thoughts on TC and Bees. I love the stuff you can get from TC such as the levitators, WOET, warded stuff, thaumium grafter (with Repair II it's a God send for Forestry tree breeding) but the aggro involved in getting it is just ridiculous. I had a serious go at it a while back and lasted all of half an hour before rage quitting it. Can't remember exactly what I was doing but I vaguely recall it being something to do with researching metals. I'd tried everything obvious and not-so-obvious and it still wouldn't work. I later found out from our resident TC guy that the metal I was trying to get needed.... wait for it... apples!! WT actual F?! I mean come on man, seriously?

That was about 3 months ago and I haven't touched it since. If I need any TC items I just get someone else to make them. I may go back to it at some point but I'll be using the TC3 wiki which tells you exactly what you need for each aspect.
I can relate to your bee problems as well because I was in that exact same spot just a few weeks ago. I'd get as far as a common or cultivated and they when trying for the next one I'd lose the cultivated and be back down with a Forest princess or some crap. A bunch of bee experts on here guided me through it though and I understand how it works now. Basically (and what none of the wikis or youtube "tutorials" tell you) is that for each new species you get you need to cook up a stack of pure drones for that species before trying for your next species. That way, if you "lose" your princess and it mutates to another species, you can put her back through with some of those pure drones you cooked up and after a few life cycles she'll turn back to what you want. You use the same method if you want to clone a princess too. Say you want to add a 2nd line for royal jelly producion with imperial bees. You can take any princess, such as forest and with your stack of pure imperial drones you can run them through an apiary and you'll eventually get a pure imperial princess after a few runs. First run you'll probably get a forest-imperial hybrid princess and an imperial-forest drone. Run the princess through again, but with another PURE imperial drone. If you're lucky the princess will mutate to an imperial-forest hybrid and probably a drone of the same (if not, run her through again with another PURE imperial drone). 4th or 5th time you should find that she's now a pure imperial princess. Make sure you use your beealyser after each life cycle to see what the active and inactive traits are. When they're both the same then it's stable ("pure"). Use soul frames to increase the chances of a mutation, but only if the mutation is listed on the neesirojgaming bee wiki, eg. if you're trying to get nobles then use them with a common and culti as it will greatly increase the chances, but if you were trying to turn your forest princess into an imperial princess with some imperial drones then soul frames don't do anything there; what you'd use instead are chocolate frames as these kill off the bees quickly which means you don't have to sit about waiting for them to die naturally.
Once you get your head around all that bee breeding becomes 1000x easier. Get some tropicals running for the silky propolis which you run through the squeezer again for a chance of normal propolis and then make yourself some apiarist pipes to automate the production. Put a wood pipe on the back of the apiary with autarchic gate (redstone signal off : energy pulser), stone pipe connected to it down the back of the apiary, apiarist pipe connected underneath and then another pipe off that to a chest or something. Set the white filter on the apiarist pipe to "any bees" and set whichever filter to your chest to "anything". What will happen is when your bees die they will all get pulled out by the autarchic gate and the princess and drones will be re-inserted in the bottom and any items/combs will go to your chest.

At basic level you want to have tropicals running for propolis for more apiarist pipes and also marbled/meadows/forest bees running for honey drops (30% chance) for your beealyser. Commons are 5% better for honey production than those (35%) and cultivated are 5% better than commons (40% chance).
You'll have your imperial bees in next to no time!
