While there may seem to be an obvious winner in this contest both options have pros and cons that we will go over.
First, we will go into the pros and cons of wood flooring. Wood flooring is thicker and less conductive than aluminum, making it a slightly cooler option when traveling in the summer months. It is a very long lasting flooring option as well. Because wood floors in trailers generally use treated wood and have gaps in the planks to let moisture out, they are resistant to rotting. This makes them low maintenance because the urine drains out. In many cases the floor of the trailer will last as long as the trailer itself. If the wood does get to the point where it needs to be replaced it is relatively easy to pull out and replace without the need for special tools. It is also very cost effective to replace in comparison to the price of aluminum. Wood floors are known to be more vibration dampening than aluminum because they are less rigid. Because of the gaps in wood floors they do let in dust when driving down gravel roads. The gaps can be sealed up but that does prevent the urine from draining so more care will be needed to prevent the wood from rotting.
Aluminum flooring in trailers has come a long way from when they were first introduced. Initially, all companies used a thin roll-on aluminum floor, and spaced the I-beams closer together to keep the floor from sagging under the weight of the horses. The issue with this type of flooring is that if it is not properly cleaned the urine that is caught under the mats will start oxidizing the aluminum, weakening it as the oxidization process continues. Eventually this causes pitting and holes in the floor. Most manufacturers have moved away from this style of floor to a much thicker interlocking aluminum plank floor. Because this type of floor is thicker it takes much more time and urine to cause any significant oxidisation. Due to the issue of aluminum oxidising and pitting over time when exposed to urine, it is always recommended to clean under the mats after every use. Both types of aluminum floors are sealed very well from dust. This is one advantage makes a big difference for the health of the horses when traveling on gravel.
Both types have their pros and cons so it is up to the buyer to decide what is the best option for their needs.