In order of longevity and maintenance Aluminum is first, fiberglass is second and rubber is last. Cost wise rubber is the cheapest to apply and the most expensive to replace (because you will have to replace it at some point if you plan on keeping the unit any length of time). Fiberglass, holds up well but aluminum is forever barring damage.
I have a one piece fiberglass roof on my unit. Other than washing it, no issues in 4 years. My last unit had an aluminum roof and when I sold it at 13 years old, the roof was as good as the day I bought it.