What you did with the Bondo was perfectly reasonable. A better product would've been that other variety of bondo that has the fiberglass strands mixed in...well...sorta better. That stuff destroys sandpaper, so you kinda apply it more minimally, and then slap regular bondo over that to get a surface that can be sanded smooth. But I digress.
Superglue then paint actually can work for small cracks. There are just a couple problems with it. It tends to be far too thin to use for very much beyond a hairline crack. Most formulations are designed to seep into cracks via capillary action, so you'll often get a concave surface. You want a convex surface that you can sand smooth. The problem here, is that even if you do get a convex surface from superglue, the stuff is very hard when cured. Harder than the fiberglass resin. So when sanding, it is very easy to start sanding away at the fiberglass resin when you mean to be sanding the superglue flush.
Spackling paste is a little less flexible than the bondo or epoxy clay. But for small asthetic cracks, it can be used.