First off you might not want to saturate the bus with data transfers. On the other hand if you are syncing you want the transfers to go as fast as possible. TB allows for this and will be fast enough into the future at least for a few years.
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Originally Posted by
tipoo 
The USB 2 micro USB connector is limited compared to the 30 pin connector, but what about USB 3? I think there was also a rumor of magsafe-like connectors a while back, these two go hand in hand. But I'd still prefer something I don't need to keep unique cables and accessories for.
The 30 pin connector has a lot more going in and out than just USB.
The issue with TB cables is real, no doubt there. However I don't see Apple going TB only any time soon. They have already patented a dock connector that maintains USB capability.
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re:thunderbolt, meh, none of these devices has fast enough NAND to saturate USB 2 and won't for a while, let alone USB 3 if they finally switch to that after Ivy Bridge macs are out. I guess it could charge them as fast as a 10W power plug, but you would not see crazy transfer speeds just by changing the connection.
Don't forget USB demands a lot from the processor which is significant on iOS devices.
Frankly I'd like to see Apple add a connector, probably the micro USB standard, for power/recharge. Like you a standard port is desired that would allow for easy connection to all the USB based recharging sources. This should be doable without stressing the design of the iOS devices. The goal is recharge anywhere, be it at home, in the car or out hiking. Ideally the port would remain active while other devices are plugged into the dock. That way high drain dock devices wont impact the battery as much if you are hooked up to an alternative power source.