Looking to buy our first horse trailer (probably a 2H BP straight load)as our 9 year old granddaughter will be competing in the spring on her pony. We also have a Morgan horse, but that's another story. Confused as to which type of flooring is better. Read that aluminum has to be acid washed; wood rots. Also read about rubber flooring which sounds good, but as we are looking for a good-condition used trailer, that may not be an option. Any feedback?

Each type of flooring has its advantages and disadvantages.

Of those you mentioned. Bare Aluminum is attacked by horse end products. Most alum floors will have mats. These mats HAVE to be pulled out and the floor washed out. (Plain water, not acid washed!... The acid wash is for the exterior skin's appearance) The mats are heavy and hard to handle. Wood floors also rot in the presence of Horse EP and water. Their advantage is in replacement. Less cost than the aluminum. Rubber flooring is not the ultimate carefree item either. Consider the metal structure under the rubber...
In purchasing any used trailer, inspect the floor condition very carefully. It could be expensive not to.