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Probably both. The early Pocket PCs were serial, then they included a USB interface but I believe it was still driven by the serial controller. Perhaps that still has some relevance, I'm not sure.
In addition to that, USB tends to have a high potential throughput, however it relies on the CPU of the computer to do the transfer, as opposed to something like Firewire which has dedicated ASICs to do most of the processing. This is why on paper USB is faster then FW (480Mb/s vs 400Mb/s) but in practice FW tends to out perform it. So maybe the Axim just doesn't have the horsepower to really crank it up.
Or maybe it's a combination of all those issues, I'm not sure :)
I use Wifi as my primary choice for transferring large amounts of data and find it very adequate.
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