Some consider there to be 5 or more levels. Breaking out of grabs. In my opinion, there is nothing wrong with studying the first level to the point that those applications become part of the practitioners' subconscious. But let's not forget that Shotokan and most other styles of karate up until about the 1920's involved practice of kata only. Regardless of what is more traditional, there is definitely value in devoting at least some time to the study of the deeper levels of kata application.
Some moves have more than one possible application for a given move.
Some moves can also incorporate weapons' use. Some moves can involve applications that deviate slightly from their basic kata form, but a large deviation should not be necessary. These are just some examples of possible applications. There are more, a lot more. During intermediate move, opponent grabs right wrist.