Yes, After Effects is used in "the industry". It might not be that prevalent, depending on what job you want. But, I can't imagine any good employer turning up their nose if you create good work with After Effects. Learning a new tool is secondary to making excellent work. I remember reading way back (might have changed now) that applicants for being an animator at Pixar are not required to have 3D animation experience. What?? Traditional (2D) animation is sufficient. Why? Because learning the tools is secondary to being able to create a convincing performance. The principles translate. That's why the question of whether AE is used in the industry is somewhat moot.

You want to make a ninja fighting a robot in 3 weeks. My suggestion of a compromise would be to make one shot of that (e.g. a ninja flourish and a quick zoom in to the eyes), just a few seconds, but it will be much better executed than a full story arc. Also, I don't know what visual style you want, but go non-realistic. You'll have more freedom and it can be just as engaging to have a blocky cartoon style or whatever.