Hi, sorry for the delayed response, and thanks for relaying your experience and fix to the communities! You're right, the Pi3 appears to pull noticeably more current than previous generations. In my experience, even CM1 was iffy- I would need to use a powered hub or a short cable on a USB3 host port to get reliable results.
A custom powered USB cable (similar to how our PiDrive Cable powers the PiDrive) would be the most certain solution. We'll work to make this happen, but it may take some time to tool. We need to find a low-mid volume rapid-tooled cabling vendor for projects like this.
It would be good to understand the voltage drop on the USB 5V for different setups (with and without hub, long/short cable, etc.). I've used some relatively inexpensive in-line USB DMM's but I don't know how accurate they are or how much they may contribute to the voltage drop. I'll try to do some research and see if there's a good way to do this (I'm not an EE, which may be obvious!).
If you can provide details of the equipment setup that's working for you (i.e. hub type/mfg, host PC info, USB2 or USB3 host port, cable length and mfg), that might help. A photo of the setup would help too. If you think of experiments and would like to test additional product, email me and we'll try to get you set up.