Hello!
Firstly, great thanks for this mod.
I was interested in mechanics of mod so I started testing.

Let's assume, 'bee factory' produces x Clean queens per cycle (cycle = 30 seconds).
To do that factory should produce x Clean larva/cycle + 50 * x Royal Jelly/cycle + 20 * x Honey/cycle.

Bee factory setup: 10 Nurseries in chain (first Nursery receives Clean queen, produces Clean larva and puts queen in next Nursery; second Nursery does the same and so on).
Each Nursery can support up to 5 Apiaries (Apiary requires 10 seconds for craft, Nursery - 2 seconds).
Each Apiary can support 1 Hive (crafting time of both machines are equal).
And 2 Apiaries can support 1 Liquiformer (last requires 2.5 seconds/craft, but has crafting speed 0.5).

With such setup bee factory can't produce more than 15 Clean queens per cycle (30 sec), because Nursery takes 2 seconds to process queen.
To create x Clean queens per cycle, factory requires x Clean larva per cycle.
= 1 Nursery is enough to do that.
To create 50 * x Royal jelly per cycle, factory should produce 2 * x Clean bees/cycle = 2 * x Clean larva/cycle.
= +2 Nurseries creating larva to process one into Royal Jelly.
To create 20 * x Honey per cycle, bee factory should produce 40 * x Clean combs/cycle = 4 * x Clean bees/cycle = 4 * x Clean larva/cycle.
= +4 Nurseries creating larva to process it to Honey.

TL; DR.
Summary: 7 of 10 Nurseries (+ Apiaries, Hives and Liquiformers), which is 70% of whole bee factory, work just for keeping factory running (read: produce nothing).
Efficiency of whole setup is 30% - that's definitely not enough to keep up factory of resource bees.
If you repeat these calculations for resource bees, you'll end up with similar result.
Also: increasing number of larva produced by queen (= number of Nurseries) doesn't help much.

So my suggestion: reduce cost of:
- Clean queen: from 1 Clean larva + 20 Honey + 50 Royal jelly to 1 Clean larva + 10 Honey + 50 Royal jelly.
- Resource queen: from 1 larva + 10 Honey + 25 Royal jelly to 1 larva + 5 Honey + 25 Royal jelly.
With such values efficiency of factory will become 50%.

P. S.
I didn't take into account modules and beacons. I build simpliest (by tech-level) setup.
If you want look at screenshots/blueprint - just let me know.
And sorry for my English - it isn't my first language.

I think you're right, 30% efficiency is a bit low. The reason I set it like that originally is because the factory only requires power, but bees have always felt a bit under-powered in general. Currently, you can get about a 1.5:1 power gain if you burn coal bees, and I don't really want to let this get out of hand, (Bees should be for resources, not power), so I'll probably buff the efficiency by about 20%. Thanks for you interest in the project, it's nice to know people would go out of their way to try and improve it.

Also, don't chain 10 nurseries in a row, just cycle the queens inside one or two :P

https://factorioprints.com/view/-LBfVclks5go4FJgpMax

@micromario
Thank you for response.
After more calculations I found some interesting details:
- With current recipes queens should produce at least 11 larva. 10 larva is enough for Clean queens to keep factory running (but this factory will produce NOTHING). With 11 larva/queen factory for Clean bees produces enough Honey to keep factory for resource bees running (but only with basic recipe - 10 resource combs per bee).
- To allow advanced comb production (25 resource combs per bee) with current recipe costs, queen should produce 16, 21, 26, 31 (and so on) larva.

And about chaining Nurseries. I know about such small setup. But I prefer use produced larva directly - without transporting it somewhere (by building Apiaries and Hives on top of Nursery).

Also, if you don't like idea of gaining more energy from bee factory, than it requires - you can just make recipes for coal harder (like it's done for uranium) and bump output for other ("non-burnable") resources.

Making coal (and other burnable ores) more expensive isn't really what I wanted to do, because power is only one use of the material. For example, it can be turned into military science and oil in vanilla, and slews of modded products. Two solutions I see for this are:
1. Making the bees process require more power
2. Editing the coal produced by bees so that it can't burn.

It doesn't seem right that ore bees are unproductive, since they run completely on clean bees which come from a positive loop anyway. It's worth noting that I (think I still) have a mod setting that lets you change how much larva you get per queen until I publish another update.