The paint system I have used in the boats I have worked on is a simple alkyd paint. For decks I clean them using a pressure washer, acetone, scraper, sand paper, etc to get them clean, smooth, remove old paint if any, etc. Use a thinned(a bit of paint thinner) alkyd (oil base) primer then finish with a couple of coats of thinned alkyd semigloss or your preference. Make sure you paint the edges to cover any exposed epoxy. This is not high tech two part paint but is inexpensive, easy to apply, can be removed easily, and stands up well. I have used this paint for hulls but have rolled it on and then wet sanded to a smooth finish. This can dull after a while and perhaps waxing might keep the appearance up.
This is not a professional finish but is adequate for my tastes. Gel coat is always preferable to paint. Many of the boats I have worked on have been painted sometimes more than once. Judging by the original gel coat colors I can see why.
If appearance is important, two part paints applied properly will give a superior smooth finish. There are also some one part urethane paints that can be brushed on to a smooth high gloss finish. If a perfect finish is important do some research into paint and proper application techniques.
Remember painting will add weight. Perhaps a few touched spots on the original gel coat isn't so bad!