Well from what I'm hearing the 9700 doesn't have enough memory to cope with OS 6 which is a big disappointment. Not sure what the 9650 has but if its 512mb then its definitely the more future proof.
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I think it also depends on the carrier which device is even available. GSM or CDMA determines one or the other (unless you play special games to unlock the cdma for gms use in US)
The 9700 is a GSM device, the 9650 is a CDMA device. The 9650 has double the memory, but the 9700 should also run OS 6 from what we have seen. Keep in mind a lot of the OS 6 stuff is rumor at this point, nothing concrete saying that the device needs 512 to run it.
The features are very similar on the two devices, they just have different form factor, some like the smalller design of the 9700 and some like the larger of the 9650.