You can get a primer to put over epoxy that gelcoat will stick to.
When you put new poly on old poly, you get a physical bond, and alot of that is determined by how well you prep it. You don't get a secondary/chemical bond. The old glass is chemically "done" a couple weeks after the boat is made, and the new glass just fills in the roughness in the surface that you prepped.
Epoxy on old glass actually gives you a much stronger physical bond, and it also has a secondary/chemical bond which is stronger that the old poly it is attached to.
From a strength viewpoint, epoxy is much stronger, it cost about double, but you don't need as much to get the same level of strength. Epoxy does not have the outgas fumes that poly does, and wont make your head hurt for days after breathing over it.
You just have to be careful about materals used. I have put 3m vinylester fairing and high build on top of epoxy, and put gelcoat on top of that with no problems. If it's above the waterline, I don't think it's as picky, below the waterline is a different story.
www.boatbuildercentral.com is where I get my epoxy and they have GREAT tech support on materials and repairs on their message board.