I suppose the first thing to do would be to make sure that the gelcoat can't be buffed out. Old Town used a rather thick layer of colored gelcoat (polyester resin mixed with pigments and a bit of filler) on the outside of the boats. It oxidizes on the surface, but there may be enough there to wet sand it up through the grits (up to the 2,000 grit range) removing the dead stuff and then buff it out. In the process, deep scratches could be filled as needed. The advantage to this approach is that it's harder and more abrasion resistant than most paint would be (as well as being able to maintain the original finish). Gel coat sometimes gets small cracks in it which usually don't really hurt anything, but whether or not you want to live with them, fill them with new gel coat (tedious) or fix them with filler and paint over them would depend on how bad they are.
If the old gel coat is too far gone to bother messing with, then some filler and a fresh paint job may be a better option. There are pre-mixed epoxy fillers like "Quick Fair" available or you can mix your own with resin and filler powders. Clean out the dings, over-fill them slightly and then sand the entire hull smooth. 80-100 grit on a random orbit sander will give you a decent base for most enamels. It has enough tooth for good paint bonds, yet will be smooth enough to give a nice finish and good gloss.
One-part marine enamels like Interlux "Brightside" or Petit "Easypoxy" will yield a surface that has similar gloss to the original gel-coat and they're fairly easy to apply (sprayed, or rolled-and tipped out with a brush). The drawback to them is that they respond to running over rocks like any enamel will, and scratch fairly easily. You also don't want to leave the boat sitting in the water for several days straight as enamels will peel. This isn't a problem with the type of day-use that most canoes get. If you figure that like any canoe, it will probably get some scratches on the bottom but the rest won't get much abuse and will stay looking good for a long time, then these enamels might be a good bet. Scratches can always be fixed with more paint.
The two-part, linear-polyurethane enamels (Sterling, Awlgrip, Interthane, etc.) are nearly as tough as gel coat and would be the highest quality finish, but are also the most expensive and the most toxic. If you spray them, you have to have a hood with piped-in air to breathe and essentially should be wearing something that looks like a space-suit. There really isn't much of a fudge-factor with these paints when spraying as they can actually kill you. You can, however, apply them with a thin roller and tip out the bubbles with a brush and get a finish that most folks will think you sprayed. By not blasting the toxic fumes all over your work space, the safety issues can be brought down into a more reasonable level of masks, gloves and good ventillation.
All in all, I'd probably go the one-part route (I usually use Brightside). The enamel finish is tough enough to last as well as that on any wood/canvas boat or a stripper and it's not all that hard to touch-up any bottom dings that really annoy you.
For the inside, I doubt you'll really need to go the epoxy route unless you have damage that needs to be repaired. You could certainly roll a thin coat of epoxy on, but it would need a UV resistant top coat (varnish) and most epoxy is pretty thick, like syrup. On exposed weave, it's tough to get a nice thin coating. I would find a nasty-looking test section (a couple square inches is probably plenty) and dab a little bit of polyurethane varnish on it to see if it will do the job without any resin being added. For the same weight and thickness of a single layer of rolled-on epoxy you could probably brush four coats of varnish or clear coat and spray eight or ten. I suspect that a couple coats of varnish or auto-clear-coat, brushed or sprayed will do all the sealing that you need. We used to get pretty good life on strippers by leaving some weave in the bottoms for traction and just varnishing it with the same varnish we were using on the outside of the hull. It was decently tough, easy to re-coat if needed and provided an adequate barrier between bare feet and the raw fiberglass.
