When you're in college, you're not there to learn about PIC or ATmega or any other specific product; you're there to learn how to use a microcontroller to solve a problem. When you're in the real world, you'll do the math (e.g. like Osgeld says on cost of components vs. size of the run), look at the standard tools your company/group uses, or maybe just "use X because we've alway used X". If you and your prof did your jobs, you'll know enough about solving problems with microcontrollers that you can adapt to the specific tools at hand.
-j