This has come up before. The fact that multiple schedules cannot currently be interleaved looks like it might be even worse on Water As Needed, since you're now recommending creating multiple schedules - one for each set of like zones.
I know you've said that interleaved schedules is "not easy" (http://community.rachio.com/t/long-run-times-following-best-practice/1329/6), but I think you've got to figure it out to avoid this non-intuitive result. I also know that, in general, the scheduling problem is (NP) hard (https://en.m.wikipedia.org/wiki/Job_shop_scheduling etc.), but it seems like a heuristic based on filling dead times as available and maybe letting soak times push out a bit would let scheduled interleave to some degree. Rather than queuing up entire schedules, you might queue up each watering duration (split by cycle soaks), not queuing up a new cycle soak duration until 1/2 hour after the previous one ran, etc. In the worst case, the combined schedules would run as long as they currently do, but that would be the odd case. Most of the time, I bet it would finish significantly sooner. Some people might be confused when their individual schedules don't start at the scheduled time, but that already happens with your current queue anyway.
This kind of thing is what a smart system should do. It is going to seem dumb to more people that just us in the forums: "Hey, why aren't any of the sprinklers running right now? It has several more zones to water and it's just waiting to let one soak? How does this 'smart' system not know that no water is running now and use that time to water something else?"
If nothing else, you guys should sponsor a university research group to investigate this type of scheduling problem. It would make a nice research paper (I couldn't find a scheduling problem online that was quite like this). They might come up with an elegant solution - or at least bound the problem mathematically so you know the limits and potential downsides.
Okay, rant over. I think you guys have an awesome product and trying to match everyone's needs and keeping it simple is a crazy difficult problem. I appreciate your level of involvement in the community here, too. I've never seen a company this responsive and willing to incorporate user feedback. You guys are rock stars!