Just read the whole thread in one go. Great read, lots of opinions and experiments. I have a few thoughts, biographical notes, and some questions.
When I started brewing, moving to secondary made a big improvement in my beer. In retrospect, it forced me to slow down and resulted in clearer beer just from more time. One of the biggest things I'm taking from this thread is "don't fear the primary", as in use longer times. I appreciate now the folly of my early attempts to bottle after <2 weeks in primary.
Even at almost 350 comments (at least 100 of which were on-topic), I don't think we've come anywhere near exhausting this issue and I'd love, for example, to hear Chris White's opinions on some of this. Temperature and yeast strain, for example. Here's an absolute worst-case scenario: -- 85F primary of a saison in a plastic bucket, into bottles that will be cellared at 75F and transported by bicycle to the location of their consumption (e.g. shaken up). These super-attenuative farmhouse strains take a long time settle out and don't form nice compact cakes in the bottle, so I'm looking at 2-3 months in a very warm primary to clarify. My two concerns are oxygen diffusion (which is temperature dependent) through plastic leading to high yeast metabolism or oxidation flavors in a delicately-flavored beer, and general yeast health due to prolonged high temp. This is just to say that this scenario is much different than 6 months primary bucket at 50-60F with a stout or porter full of antioxidant melanoidans sitting on a nice, compact chico yeast cake. I'd love to see, for example, calculations of oxygen diffusion rate curves through plastic buckets.
Back to my original comment about short primary, I feel like some of the secondary oxygen-exposure issues are ameliorated by transfer to secondary before you hit FG. Yeast are always happy to consume any O2 that's available, and will do so quickly if they're metabolically active. So I feel like there are 2 separate issues -- if you're going to go to secondary, it doesn't make sense to me to wait until you hit FG, just get off the trub early and let things clarify in a nice, sealed carboy. I think of this as the "set it and forget it" principle -- once it's in secondary, I can neglect it as much as I like. Bottling is similar, you're waking the yeast up and giving them some sugar to chew on, and they *should* draw O2 levels in the bottle down to almost nill. This is simply me reasoning through things; I have no first-hand *evidence* for any of the above. By my logic, 02 absorbing caps look a little suspect, and I have seen passing reports of their preserving the "hop-head" of bottled beer.
That said, I see some extended primaries in my immediate future for chico yeast. The evidence in this thread alleviates my "get it off the cake" anxiety, which gives me yet another method to "set and forget".