> ...my orders with free shipping due to price threshold tend to be significantly slower than Prime, often taking weeks for items of all Prime eligible items.

I've had the opposite experience (and posted about it here before). Since I joined Prime last year, I've had issues with the guaranteed 2 day shipping taking 3-4 days or sometimes a week. I don't live in the backwoods either; I'm well within the Atlanta metro area (though not quite inside the perimeter). Before I joined Prime, even a non-Prime eligible item would tend to arrive in 1-2 days.

I did call Amazon about the issue several months ago, and they offered me gift card credit equal to the non-Prime shipping cost of all shipments that didn't meet the guaranteed date, and since then I've only had one late shipment. It definitely pays to contact them about it; I know from working for a company that sells on Amazon that the customer is treated like royalty whenever there's an issue, whether it's with Marketplace or Amazon direct sales.