Composites: In recent years some manufactures have made more composite flooring options available. There's been a effort to meet customer demand for a decay proof deck material without all the structural drawbacks normally associated with aluminum decking. Composites are made largely made of recycled plastic products formed into panels similar in size and thickness of wood. Composites are far superior to aluminum in insulating qualities. Rigidity is generally superior to aluminum but still inferior to wood. Earlier versions did over time suffer from sagging. However the later composites panel decking has fiberglass reinforcement that has corrected these concerns. However this piece of mind does come with a price however, for composites often is a more expensive option if available.
Aluminum: Is available as a deck material from various pontoon boat manufactures. Aluminum is generally offered as an option to ease customer fears of woods potential to decay. And aluminum does offer peace of mind for the customer and has become a major marketing tool for those manufactures that offer it. However when considering some of the desirable characteristics described earlier, aluminum does indeed have some shortcomings to consider as a deck material. Aluminum has poor panel span strength and rigidity. To compensate this most manufactures lay aluminum in sections of pieces six to eight inches wide. While in comparison other materials are generally four foot wide sections. To cut costs many manufactures also use self tapping screws to fasten it in place. All the additional seams also result in an increase of stress and wear on the carpet over time. Aluminum also has poor insulating qualities of both sound and heat. But there are many people who feel that the prospects of no decay over ride all the negative aspects of this material.
Wood is the most traditional of all the decking materials. In almost all the above desirable characteristics it has the most desirable qualities. Wood also has the greatest rigidity and panel strength of all the available materials. Its insulating qualities are as good as the composites. It's also one of the least stressful and maybe best substrates when used with carpet. However wood can, have and does exhibit decay. Like any organic material if it's left untreated it will have poor survivability in a wet marine environment. Therefore you should be certain that a good grade of marine plywood was used in the construction of your boat. If marine grade CCA treated 3/4 in. plywood was used in construction and some general care was taken of the boat, you can rest assured that you'll get many years of relatively carefree service from your pontoon boat purchase before any issues or observation of any decay.
Excerpt taken from a longer article on - http://www.pontoonhouseboatodyssey.com