1. They originally wanted Spike in a stand alone series, but decided they liked Spike with Buffy and the other characters -- pretty much the sort of thing we saw in the first ten issues.
2. As they were breaking down the details for the next ten issues, they realized as they hit the big plot points, Spike wasn't showing up in them. It'd be Buffy does this, Xander does that, and Xander, Koh and Spike do that. Nothing specific for Spike. They didn't think it would be doing a service to his character just to have him around doing good dialogue. And there were Spike-specific issues that were interesting to them to explore but they couldn't do it in the main book. Ergo miniseries.
3. All the pieces of season 9 work together in complicated ways. It's not one big story, but all the pieces are important. That means A&F and season 9 are NOT running on separate tracks -- though the way they fit together is not what fans might think. This is true of the mini series as well. We won't see the big picture until it's all done.
4. They have never adjusted the story to manage sales. That's true of the pregnancy, the abortion, the non abortion, Spike's presence and Spike's absence. They feel like the best they can do is bring in good talent to tell a story true to Joss's vision. If they were pandering to fans to juice sales, it would be in the other direction -- Spike is very popular. I'll add that Scott's pretty excited about how the story works, and he writes about it in a way that is 100% consistent with the thought that they write the story as best they can and hope the sales will follow.
5. This was a big change, but they thought it was best for the character and best for the books, and probably best for Spuffies.
My take away... this is about the plotting of the midsection of the season. It's not a big shift in whatever they were planning for Spike and/or Spuffy. It was the dead zone for Spike that got them to change things, not them changing away from something that was well-thought out. They hadn't realized until they broke it down that there was nothing substantive enough for Spike. I like that their interest in the character caused them to think about how they could get more of Spike's story out there when it wasn't going to fit in the book.
ETA: Scott adds that he's sorry he hasn't had a chance to reply to everybody -- he's been really busy.