I use bikeflights pretty much exclusively for my USA domestic bigger-box shipments, mainly wheels, frames and complete bicycles. I usually ship complete bikes in two boxes. I have a now-dormant FedEx account, and when I regularly checked rates when first using bikeflights, they were always cheaper than my FedEx-direct rates. My FedEx account is a low-volume individual account, so folks who work at places that ship real volume might get competitive rates through work. We're a low-volume FedEx shipper at work, so bf is cheaper for me than work.
Keep in mind that bf is using FedEx Ground, which typically needs a 24hr lead time to arrange pickup. Pickup only costs an extra $5, but I usually drop off because I don't want to delay the shipment waiting for the pickup.
I've never had issues with bf on domestic shipments, but did have issues with international shipments, but for non-bike items at work. When I do a domestic shipment, even at stupid-late hours, the label usually comes back within minutes. I've had to wait a full day or more for customs docs/labels at work, but again, this was for non-bike items, which might have slowed them down.
BF will ship just about anything btw, they don't care whether it's bike-related or not. So if you need to send a big box to yer uncle across the country, they'll ship it for you. They are limiting their Protection Plan coverage (which, btw, they state is NOT insurance---prolly some legal coverge thing there) to bike-related items, however. So I can't use them at work anymore.
I find, in general,that USPS is cheaper for int'l shipments than FedEx/UPS, but USPS has stricter requirements for box sizes, so shipping complete bikes via USPS can be problematic. I almost never ship big stuff internationally---every time I try, I quickly regret it. YMMV.
Yet another tangentially-related BTW, our self-insurance policy at work does will not cover international FedEx shipments. USPS/UPS only. The agent said something about higher losses with FedEx, but I suppose there could be something else happening behind the scenes?
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Fuggedaboutit!