One of the core reasons I use Forestry is because of renewable resources and sustainable energy. That was always its main selling point, the whole reason I picked it up back when it was just a sub-forum on the BC forum and a wiki. This and your multiblock farms running on non-renewable Fertilizer made exclusively with Apatite (at least non-renewable on it's own, without other mods to add in other recipies which are renewable) makes me wonder if you are moving away from this principle.
Indeed, I find myself using MineFactory Reloaded farms these days powered by an Engineer's Toolkit hydro dam. The Unifier will not change fertiliser I guess it's not forge unified.
Forestry had always been my 'renewable' key component in my automation. These days, it is reduced to occasional use of the electric engine, and the moistener for making mossy stone for TiCo. I have not done the bees thing for a while though I'm giving it a revisit now.
From the beginning I loved the 'green' concept of Forestry, I was even content with the humus requirement (yay for old school autocrafting from Buildcraft). With addons like magic bees and extra bees sure there aren't many non fully renewable resources with bees alone. I find that the landscape of MineCraft mods has shifted, where Forestry was once the groundbreaker and thus the only option in renewable automation it's competition both for the 'green' and 'renewable' titles has stiffened. Sure the server I manage has Extra Bees and Engineers Toolkit more than the Direwolf20 pack, but the DW20 modpack has so many ways of doing the same thing now it's sometimes hard to choose. Thermal Expansion has lovely self ejecting machines, though IC2 with overclockers and extra management can do the job faster. TiCo seems to be the only way to process Aluminium at benefit. Applied Energistics rocks, allowing a NEI save to carry everything you own between world restarts. The balance between work and reward is probably the crunch point here, the multiblock structures and the electron tubes genius as they are add complexity. If I was in a game with 'just' Forestry there would be no problem, my game now is more about optimising the integration of the various mods rather than just doing things using just one mods route to a goal. Forestry still 'eats' capsules same as IC2, but with TE I can use the capsules again. AE's many functions mean I need one 'pipe' to carry well everything (even without EnderIO). Just please make AE2 forge multipart friendlier (for pipe coverage)! Ars Magica 2 removes the need to constantly charge tools apart from specialist bits, Projectile - Dig is still faster than a quarry. I find that the focus is leaning towards the 'merging' mods that go the extra mile to work with the popular base mods. AE, Modular Powersuits, Magic/Extra Bees, Engineers Toolkit, Thaumic Tinkerer and Denoflions work are prime examples of intermod support (I guess Bibliowoods should be here too!). I've excluded the awesomeness that is Forge and the support it gives with common ores, and the various pipe providers like Buildcraft and TE.
MFR and TE now cover almost all my automation needs, maybe with AE for storage. Modular Powersuits rocks for minimising carried tools. I think I'd be happy with just them in SMP till I ran out of things to automate. Then I'd look at bees and magic. Thaumcraft is awesome but with the other mods for automation and management it's only really good for automating itself. Ars Magica 2 has renewed my interest in 'magic' mods mainly as a new source of 'power' as mana, no need to recharge the mining tool!