Wire crates are better for ventilation and fold flat for easier storage and transport. They are also easier to clean because you can just slide that tray out and scrub it. The plastic crates are a lot sturdier. Unless you have a little purse-dog, they are a must for airline travel. If you live in a tornado prone area it's a good idea to have plactic crates for all your animals in your tornado shelter. If your house is blown away or collapses, that crate will protect them from being hit by debris or from panicing and running off. A wire crate will bend and jam the door, but a plastic crate will dent or crack and can be popped back out to free your pet. If all else fails, it can be unbolted and taken appart to free the door or get them out.
