I don't use the quarry because I agree it's not very engaging to play with. Actually, at the moment I don't do any automated mining, but when I do use automated mining I like RP2 frames and/or turtles. Frame machines are fun to build and turtles are sorta a custom difficulty setting depending on how much program you do vs. using someone else's program. I kinda want an arcane bore and a cart with a galgadorian drill just because they look cool, but neither of those is really about the resources they generate - at least not for me.
I don't use the filler mostly because I have a bizarre fondness for clearing areas manually and making non-square buildings. That's a playstyle choice, though - I'm more of a builder than a tinkerer when it comes to Minecraft.
The Builder - the machine that gets paired with the Template Drawing Table to actually replicate the what's on the template - is bugged last I heard and can't even be used at the moment. However, I'm a very big fan of it - it really just lets you replicate builds you've already done without using MCEdit or cheating in resources. If you've spent 16 hours building a giant glass dome by hand, you might feel more justified in using a machine to replicate that hard work. Of course, the easiest solution is to get a turtle to do the whole thing for you in half the time without worrying about mistakes while you go have a margarita, but that's a whole different problem.
Forestry is, hands down, my favorite mod in FTB precisely because it doesn't just do everything for you. Actually, it's more complicated to get a lot of things running with Forestry than with vanilla. In modded Minecraft Forestry really stands out for how difficult it is. Steve's Carts, Thaumcraft, ComputerCraft, and RedPower all make the process of automatic farming much simpler than Forestry, for instance. You're also ignoring substantial portions of the mod like apiculture and arboriculture.
I'm not a huge fan of BC pipes, either, but there is a pretty significant faction on these forums that loathe RP2, so for them it's pretty much either BC pipes or bust unless they add something else in. Vanilla means of moving around blocks are just not up to snuff once you get used to pipes/tubes. I must also admit that, even though I'm not a fan, there are still times when BC pipes are the right tool for the job.