That is one of the two reasons I signed up for prime in the first place, I'd always get super saver and 99.9% of the time it'd arrive in 2 days. All of a sudden it started taking the full time.
I don't remember exactly what the other reason was, but it involved a one time money savings which was > the cost of a year of Prime at the time.
So I can imagine that this was originally a bug. Probably at some point they reached the capacity of things they could physically get out of their warehouse and onto a shipping truck per day, regardless of whether that truck is heading to other trucks or to a plane. So you need to prioritize, every day, the things that must go out overnight to meet the deadline. If you're full and you have things that could be shipped tomorrow, they wait tomorrow. Then tomorrow, or a week later, or whatever, those things are now on the list of stuff that must go out overnight.
Ideally your capacity isn't filled up by the must-be-overnight stuff. But if you're busy for a few days, suddenly a bunch of regular stuff turns into must-be-overnight stuff. And that delays next week's regular stuff, which then turns into must-be-overnight stuff next week. and there's no way to recover from this automatically. You could recover if you manually added more shipping capacity, or if you told customers that ground shipping would take even longer (so you can spend a few days clearing out backlog), or something.
That said given that the current state incentivizes customers to do exactly what you did, I wouldn't want to be the manager who prioritized fixing the bug....
Wouldn't that explanation only work if their load is high enough that they frequently hit the limit on how much can be shipped per day, but they rarely hit the limit on how much can be shipped per 5 days?
If the load is lower than this, then deferral of non-Prime orders would rarely be needed. If the load is higher than this, deferral would rarely help.
If their load is in that window where deferral can help with load, the amount of deferral for a given warehouse should vary from order to order all the way from no delay to several days.
My recollection from before I got Prime was that almost all my free shipping 5 day orders shipped the same day, and then over a very short time that changed to them almost all being delayed by an amount that depended on how far the warehouse was from me. I lived in the same city as their biggest warehouse, for instance, and orders served from there were almost always delayed 4 days and then overnighted. That indicates that the deferral was not based on load.
I don't remember exactly what the other reason was, but it involved a one time money savings which was > the cost of a year of Prime at the time.