The 1000's are prone to the following:
Clutch shudder
The EMS on the 1000's was problematic. Suzuki America did a recall, South Africa never. I did a techklusion chip on mine from Tornado to resolve this, money you dont want to spend unnecessary.
Bashplate for the 1000? A nightmare as you need to buy from SW Motech or some expensive oke, for the 650 you get one from Hyde, fooken solid plastic.
Only one pipe to replace with an aftermarket zorst

Lighter on fuel by far.
In all, if its you alone, go 650, you wont be sorry.
Both, both is easy to lift