I hate scratch's, too! And there is a procedure to keep the bottom of kayak looking as good as new. There's no easy solution, in my opinion, other than bodywork style, like with urethane paints, which starts with sanding and goes to a compound buffer.
Here's the low-down: for starters, I use the self-stick disc sanding pads attached to a variable speed drill. I start out with medium disc and work to finer disc, depending on the scratch. To get even finer, say 1000 or above grit, I have to cut out a 5" circle from a sheet of the wet/dry automotive sheet paper to fit my attachment disc. I use dum-dum caulk to attach them. I do this because I need to wet sand the hull with the extremely fine paper to ready it for the buffer. The dry self-stick pads are only used to remove the scratches. After the wet sanding, I use a orbital buffer with a wool fleece to bring out the luster. I load up the wool fleece with a jeweler's red rouge buffing bar. The results are absolute perfection, even better than new! Like mirror! And it doesn't take long if done routinely.
That's how I do it for minor scratches. I do not see any other way. I've heard of heat guns, melting the plastic, crazy stuff like that, but see no need for that kind of extreme approach with normal scratches and scuffs and scrapes. I use some of that KeelEasy for the keel, which is great and keeps it in check. Easy to maintain.
All in all, even after a year of extreme usage out in the rocky Everglades and throughout central Florida, hardly a scratch to be seen!