@bove: Agreed. I suggested such a thing to Vanilla IC2 a long time ago, and I feel like GT should have a breeding thingy, actually hard, random and not as easy as Forestry (which become easier once you know how to get each species) and of course less OP since it would kust help for energy generation.
I think a big tank-fermenter which would takes an unbelievable time to refine stuff into various fuels would be cool, and then adding bacterias/micro sea weeds would decrease this time while greatly increasing the energy benefit (generating alcohols, hydrogen, methane at differents ratio input/output, speed, all of that depending on the species you use). As of the breeding system, I think a GUI-mini game like the nuclear reactor one would be fun ;). But it should definitely be difficult enough so stupid people wouldn't succeed ^^.
What about a Darwin-like approach (life evoluting because of not well adapted organism dies, but you could put your own additional conditions so they devellop like you want ^^) ?
As an example, you could use kinds of food cells to help the bacteria you want to devellop, but it might as well prevent them from becoming more resistant. In the same way, light-making conponent would help but wouldn't help selecting species not needing light to devellop. Radioactive cells could be used to increase the rate of mutation but would sometime kill some cells. In the end, you'd like to impose the harshest conditions possible to your cells so you only get the bests, but you might get cells able to process fuel without light, energy (heat) or enhanced foods, but they might be less efficient in terms of energy generation than others, and you might also kill all your organism or most of them and so need to start breeding again from scratch (or almost) ^^. I even think the breeding thingy could also be the fermentation device itself. Anyway, I'm talking too much and would explain that, if Greg was likely to implement such a thing ^^.
On a (not that) unrelated note: Is someone posting on BC-forums/able to suggest stuff to SirSengir ?
Because I thought about what made bees OP compared to IC2 crossbreeding and easily found it: apart from the randomness of IC2 crossbreeding, I think the biggest differents are weeds. That's why I thought it would be nice if Forestry had a Config so Bees (and trees) can die from diseases, in a hard-to-prevent&weakening-species way, like IC2 WeedEx. But the thing is I'd also like nerfs of farms, engines and Biofuel, so I guess I'm not likely to use Forestry before a while xD