Generally, the type of samples you intend to freeze dry will determine which type of lyophilizer you should purchase. Tray dryers are best suited for small samples with a low amount of moisture, like when you're using microplates. Flask dryers are used when the sample in question has a lot of moisture to be evaporated and isn't particularly small.
There are other factors to consider, however. For instance, tray freeze dryers are known to have more precise settings for the different parameters of a recipe. This makes them ideal for recipe development and testing, or for processing particularly sensitive samples. Conversely, flask dryers are better for labs that are doing routine freeze drying with more forgiving samples.