The reboot issues are old news... the storage drivers had some bugs in 5.0.X and it caused problems when the phone attempted to wake itself up from deep sleep and the internal storage wasn't ready to be accessed. 5.1 addressed the issue. It was an isolated issue in 5.0.2 and a rare one in 5.1.
Which phone? depends on your priorities. Yes, the S6's camera is top notch, but I have no issues with the Nexus 6's shooter to be honest. It takes pretty good pics in its own right and I have no major complaints. The screen? Sure, the S6's is better, but I'm one to fuss with every aspect of my phone and a different color calibration is just a custom kernel away. Even so, the colors are fine and I would rather use the much larger screen. But if aren't one to live with a 6" phone, the S6 will work better.
The two phones cater to different needs.