A fiberglass/plywood deck will only hold up if there is only minimal flexing. I would wager that there is not enough support for the plywood, which causes it to flex, which causes the fiberglass to crack, which allows water in to rot the plywood. I don't think you should mess with rubber because it needs another deck over it to protect it (plus UV damage) and weight is a consideration. I don't think you should mess with rubberized metal because it just sounds silly. Actually, get away from your rubber ideas. It is easy to make fiberglass slip proof by adding sand or micro balloons to the top gel coat finish.
You might want to consider pressure treated plywood if you are worried about rot, but I don't think fiberglass will stick to it as well. I would put fiberglass over plywood and treat it with uv proof gel coat with non-skid finish. You might want to beef up the underlying metal framework to make the plywood spans less. Maybe have sub frames welded in to reduce the spans. How thick was the plywood, minus any glass, before? There is a real tug of war between strength on one side and weight on the other. They probably tried to save weight and didn't make the framing strong enough, or the plywood thick enough, or the fiberglass thick enough. If this is truly a boat and not a dock then you need to keep it seaworthy by keeping it light. I can't see using less than 5/8" plywood with 16" on center framing. Ideally, you would be able to use two layers of 3/8" ply with epoxy in-between and all seams staggered so that you don't have over flexing at any one joint that would crack the glass. Some good techniques at this web site: a must see: http://www.jlconline.com/jlc/archive/exteriors/fiberglass_decks/index.html Make sure to read all 5 pages. While the article is about f/g roof decks, that is basically what you are doing.