Diamond Comics has, by my understanding, had some success in getting comic shops to adopt a modern POS system, and I believe Alliance is still planning to do a similar thing for hobby shops, though I don't think they have a public timetable yet.
However, there are many more issues mentioned in my post than can be solved just by a decent POS system.
If a decent POS system was in place, they would be able to track things better, which would alleviate some of the issues. After the service tracking issues, the rest of them are really just logistics numbers that Paizo could set, if the stores didn't agree to them, then they wouldn't be eligible to set up the subscriptions.
I don't by any means think this is an easy fix, nor do I think it is one that Paizo should be putting the effort into creating. I work for a POS software company, and this kind of thing isn't simple at all...but it could be done, and done well.
It honestly is on the end of the stores that changes need to be made, because if those changes were made, the rest of the setup on Paizo's end wouldn't change from the business model that you are using currently... the POS system interfacing with a database maintained on Paizo's end would be able to manage it all, if the POS system was well written, and designed with applications like this in mind. The unfortunate thing is that most POS systems are very generic, and something like this would need to be done in a very specific way.
After it was in place - then Paizo might consider working on resolving the remaining logistical problems. Until then, I wouldn't expect you to try to do anything at all with it...it's not worth setting up for one or two stores that are capable, it would have to be something where the stores met certain criteria, and the subscription prices would be higher - and the customers would know that, and choose to do it or not.
I appreciate you taking the time to respond though! I think Paizo is doing a great job with the business model that it has - and that you shouldn't be looking to change things on your end.