It is possible to apply polyester gelcoat over epoxy resin if you take proper precautions and follow the correct procedure.
Here's an article covering a test program using polyester gelcoat over epoxy resin (West System, in this case). I have done this, and it worked out well enough as far as that goes, but I wouldn't make a habit of it. Still, it's good to know that one can use superior epoxy resins and still patch the cosmetic surface with gelcoat afterwards in situations where painting isn't called for.
Link: Polyester over Epoxy (PDF File)
The cracks you show are typical features of many boats, and are rarely harmful to the overal integrity. You could leave it alone. The previous "repair" is clearly a poor application of some cheap gelcoat "repair kit" that a previous owner bought at the marine store; not only did it not "repair" the problem, but it looks worse t han if it had been left alone.
If you want to repair these cracks for real, however, it will require grinding out the crack until you reach solid material in all directions. What material you use to fill the resulting gouges will depend in part on how deep the areas end up being. Some fiber reinforcement will help prevent the same cracking from reappearing, but in these natural stress points isn't unusual for some form of a crack to reappear (depending on the extent to which one goes to repair them in the first place).
I don't advocate using polyester resin as a repair system. The quality of the adhesion (bonding) simply isn't as effective as epoxy. For a simple cosmetic repair like this, particularly where you want to use gelcoat over the top, though, I suppose you could get by with polyester if you preferred. But I didn't tell you to.