Ventura Boat Services works with both paint and gelcoat on a regular basis. We put together this blog entry to compare and contrast the two. As far as overall considerations, the most significant issues are durability, repairability, and appearance.
Durability -- Gelcoat is thicker than paint. The gelcoat layer ranges from about 1/16 inch - 1/8 inch, while paint is about as thick as a sheet of printer paper. So for scratches and scuffs, gelcoat tends to be more forgiving. A shallow scratch in gelcoat can likely be wet sanded out. With paint, a scratch is going to show until repainted.
On a boat you will find (and spill at some point) gasoline, kerosine, denatured alcohol, etc. When exposed to chemicals, both paint and gelcoat generally both do a good job protecting the underlying fiberglass, wood, or other substrate. However, gelcoat is more porous than paint, and therefore more easily stained from engine oil, suntan lotion, wine, bird poop, etc., then is paint
Another durability issue is how well paint and gelcoat age, and match new paint. With gelcoat, color retention starts to decline as it starts to oxidize -- starting pretty much as soon as it is brought out into the sun. Once the color of the gelcoat changes, you will never be able to match it to new factory gelcoat colors. Paint will generally still match up with a new can of factory paint after 3-4 years of exposure. Repairability -- the color matching process is the last step of any surface repair on a boat.
Repairability -- Each coating is different in its ability to be fixed and touched up. The final step of any repair is paint or gelcoat. Gelcoat shines in ease of repair for smaller damage spots. A larger area repair will have better results with paint and by applying that paint by spraying it onto the surface.
Appearance-- We all want our boat to look like a million dollars. Gelcoat will look great, and many boat owners are fans. But as far as gloss and color retention and reflection goes, paint will always outshine gelcoat.