Re: bioreactor/BFG balance:
First off, MFR's stuff will always be cheaper to build because we do not have an item infrastructure ala IC2 or TE, but that is why the alternate recipe sets exist. At the end of the day short of jamming netherstars and emerald blocks into every recipe there is only so much I can do. Some people will disagree with me not adding said infrastructure, but we have enough of those and MFR is not designed to be standalone (good luck without any power transport).
I think that your design philiosophy is a very strong one, and I really approve. The cost with a Boiler is a) it's a multiblock structure requiring gated resources (steel), but that only produces the steam... you'll still need a whole pile of engines running off of it which are each purchased separately, and without them, your big steam boiler is nothing but a fuel-consuming paperweight. I really don't think you should even bother trying to match something like that.
For the bioreactor output, it was designed to be used as kind of a garbage disposal for seeds and saplings that could be a viable fuel source if properly automated. The aim was to make it and the BFG in the same ballpark for MJ per input compared to Forestry as they established precedent, but the BFG in 1.4 was barely more useful than a void pipe and Forestry changed their math in 1.5 (as well as breaking the biofuels being naturally interchangable).
Honestly, I like how the Bio Reactor works, particularly vs how Forestry now does it. People complain about TC3's research system, and Forestry's breeding system is just as big a pain to do... and it's pretty much required to get any kind of biomass out of the system.
Really, I'm also a huge fan of how efficient it is, and that it scales in efficiency with the more different types. That makes it a lot more interesting than just 'dump your seeds and go'. Or rather, you -can- do that, but if you want to get the most bang for your buck, you are probably wanting to have several different types. Personally, I'm a huge fan of using potatoes, carrots, seeds, barley seeds, oak saplings, birch saplings, and Spruce saplings. That's seven types right there, without even trying very hard. Potatoes and Carrots are used in several recipes, wheat is needed to keep my leather factory running smoothly and the seeds are just a necessary byproduct, barley is just easy to produce, then three different types of wood so I have options when creating and decorating construction projects.
As for the 16MJ/t output, it is my opinion that all the other BC power sources are too weak to realistically run a base off, especially as they tend to be rather finicky. I'm sure a lot of people will disagree with that but hey; it's configurable for a reason. I expect pack authors (hi shneeky) to make it match their vision.
And I, for one, thank you profusely for the degree of customization you offer in your mod! Currently, I've got TE compatible recipes enabled, with 'vanilla' disabled (gregtech isn't even an option, I don't have IC2, much less GT, in my mod pack), and Bio Generators producing 6 MJ/t.
I do understand where you are coming from, though. With all the power draws in a typical base (all those harvesters, planters, fertilizers, the breeder and grinder, plus my ore refining system and ME Network), a single old-school engine just won't cut it. However, in my specific mod pack, it was just 'too good' compared to any other engine, and there was a feeling of 'why bother with anything else'.
Since I like to have viable options for players, I toned it down a bit, but still kept it relevant. After all, it's a direct replacement for Combustion engines, with less lag due to less animating parts, and a better renewable fuel source. The whole 'doesn't blow up' thing is another good point there. However, I also wanted to reward players who wanted to expend the resources on on a boiler to get something for their resources, time, and effort.
However, as I've said before, this is merely what I've done for my mod pack, to try and present my players a plethora of equally viable options for power generation, and not any kind of blanket 'ZOMG OP NERF!' statment which would be ludicrous to make in any sort of an absolute sense. I've also seen mod packs which go the other route, and just double or triple the MJ output of the other engines and leave the Bio Reactor at default as the 'standard' of power generation (which is something I rather strongly considered at one point).
The important thing to take away here is: My players are reporting that they really enjoy MFR, and are happy it is in the mod pack. Also that I, both as a player and a mod pack compiler, cannot endorse this mod strongly enough. Heh, that sounds like something at the end of a political ad...
"I am Shneekey, compiler of the ShneekeCraft mod pack, and I approve of this mod."