I only have reset issues when trying to use the IGP for host graphics, with two standalone GPU's it works fine. I am passing through a GTX1080 and use a 1060 as the host GPU. What are the vendor id and hardware id (found in device manager) of the USB 3.0 controller when you pass through a device? Maybe it mimics an Intel or a common NEC USB3 controller. It looks like VMware actually allows you to use the Intel drivers now: So if you really need windows 7 usb 3.0 (not 2.0) devices you need to pass through a controller.
I've wondered if you couldn't modify the Intel USB3.0 driver package to get it to install on the virtual device, but it probably wouldn't work even if you could. It seems like they could be developed but they aren't. So while you can actually pass through entire USB 3.0 controllers to windows 7 (or hell, XP because you can install the manufacturers drivers in either case) there's no drivers for the virtual USB 3.0 controllers. Well, windows 7 doesn't have any built in USB 3.0 drivers since I don't think USB3.0 was released until a few years after windows 7 even came out. They added USB3.0 device passthrough, but they rely on the OS built in drivers for the guests virtual controller.
Yeah, this is a limitation in ESXi as well.