If I were you I would stay with a polyester resin based product, like Bondo. If you are going to do a thick application then you need to consider that Bondo can be brittle and could crack if the panel its attached to is flexed. You might want to consider "reinforced Bondo" like Evercoat Kitty Hair (http://www.evercoat.com/productDetail.aspx?pID=38 )if building up to 1/4", and then smearing with a final topper of smooth Bondo.
I have quite a bit of experience with epoxy resin based products (West, Tap Plastics, etc.) and they are always an absolute first choice -- when appropriate. However I don't think they are appropriate in your case. Polyester resin and epoxy resins don't play well together. Epoxy will stick to polyester, but polyester won't stick to epoxy. So once you put epoxy anywhere you can't come back over it again with polyester.
Stick with the polyester resin based products. They are faster and easier to use than the epoxy products, and will probably produce better results. Just make sure you seriously abrade the gel coat first (like 40 grit!).