Seriously? After all the time myself and many, many others (especially in that Combat thread) invested, you still fell back into your old habits? That's a shame, on so many levels.
So you want to get in shape before you get in shape? Man, there's always going to be an excuse why you shouldn't start, so just fucking start. Start tomorrow, start Monday, whatever. But start.
False premise. There is no "best". There's "stuff that works well". And a lot of different stuff works well.
Like Anchor said, DeFranco pretty thoroughly explained his set/rep scheme at the end of the first WS4SB article.
Here's another one of those bad habits of yours. You can always find a successful coach who seems to advocate 180-degrees opposite of another successful coach. Hell, read what Thibaudeau was writing 5 years ago and it's a world away from what he's writing now. Again, it's not "what's best". If anything, it should reinforce the fact that different methods, when intelligently applied, can be equally productive.
Because there's nothing at all wrong with using isolation exercises within the context of a well-designed program. Easy enough.
Then e-mail him or something. Not sure how in-depth you expect us to get defending or explaining the program decisions of a guy who's been at the top of his career for a very long time.