Gel coat is great for a number of reasons. Durability, buff-able, high shine is possible with buffing.
Down sides: Tough to spray, needs to be sealed from oxygen to cure (this is handled in polyester resin by adding paraffin wax to the resin. The heat caused by the cure melts the paraffin and it rises to the surface creating a barrier between the oxygen and the curing resin. This is why you have to grind resin after letting it cure out before applying a second layer of glass OR painting/priming).
NOW, when you shoot gel coat, it will flow out but then you need to sand and buff the whole body as the gel coat will typically end up with orange peel. This is very common with paint also but it is easier to work with when it is dry.
In gel coat, a solid color is far easier to shoot than a metal flake job. The metal flake process requires a black gel coat background, then the metal flake in a clear gel coat base, then top coat with more clear. This all then needs to be sanded and buffed. IF it is a good shop and they have a REALLY good metal flake painter, this would be awesome. If they say they can do it, ask to see samples of their work. This is one of the TOUGHEST "paint" jobs to do and can turn disastrous if done poorly.
The benefit of top coating your car in gel coat is that it will be a great durable finish that will contract and expand as the body does pretty much at the same rate. It will be buff-able if scratches occur etc.
OK, so with that rather weird explanation. I would get a FIRM estimate from the paint shop for BOTH finishes.
For my off road car I painted it with Enamel with a urethane hardener. The paint job held up for about 5 years. It now is about 10 years old and a lot of spider cracks and whatnot are starting to show. (I also rolled it in BAJA, bashed in to a tree etc. but it has done very well for me.
I would consider the value of the car and determine how long you want to keep the car. If you are going to keep it for a long time I would do a gel coat finish. IF you plan selling it off in a few years I would do the cheapest alternative.
Not sure if this helps. Email me with any other questions. Chris