I estimated the additional waste created by 90-day supplies at 4-5%

A recent publication from Walgreens employees suggests a lower amount of waste.  The primary difference likely results from their calculating waste only from switches to a different strength or medication.  My analyses also included patients that discontinued therapy for a condition.  This commonly occurs approximately 6 months after starting a medication.  Conceptually, a patient would "waste" an average of 15 days of medication following discontinuation of a 30-day supply.  Patients with a 90-day supply would waste an average of 45 days of medication.

I prefer 30-day supplies when a program includes an alert identification and notification system that relies on claims data.  This allows the system to identify potential gaps in care sooner than with 90-day fill intervals.

The op-ed piece in the same journal also explains some caveats related to this study.

What Patient Characteristics Influence Use of Mail-Service Over Local Pharmacies?

A recent article in the American Journal of Managed Care identified better compliance (84.7% vs 76.9%) in patients using mail-service rather than a local Kaiser pharmacy.  However, the self-selected groups had much different characteristics such as race, socioeconomic deprivation score, Medicare versus commercial insurance and financial incentives to use mail-service.   I am still not sure whether place of service matters in most situations.  I think the services any pharmacy provides to improve adherence makes a bigger difference.  These include reminders, compliance monitoring and notification, incentives and personal connections with a pharmacist.