If you want any kind of motion blur, using slow shutter speeds, you need to do a photo time lapse. With video time lapse, the slowest shutter speed you can use is 1/24.
I use FCPX and set the duration that a photo is shown to 1 frame. Flickering could also depend on the settings: i.e. if the exposure is set to auto and the light changes.
I have a Hero 4 Silver (I'm sure the 5 and 6 are similar...) and only get about 2 hours on battery. Every time I do a time lapse, I always have the GoPro plugged in to AC power. However, if you're not near an outlet, or don't have any other means of powering the GoPro, then you're very limited on straight battery power. About 2 hours. :)
