Not specifically for boating but "trackmyhike" "tracemytrail" and similar hiking GPS apps for phones do some of what you're asking. The only one I've used is tracemytrail, which is at least useable, most of the time on my Galaxy S4mini. It let's you save "points of interest" along your way but I haven't figured out a way to set waypoints prior to starting the hike/paddle session. I haven't bothered to check if it gives a time between points, but it does a decent job of tracking where you went and you can add photos and notes to the "points of interest". Unfortunately, that does mean you have to save those points as you're traveling, which could be more difficult in a kayak.