Novice question about setting system clock in microcontrollers
There are a lot of embedded microcontrollers that have no PLL, so your assumption is wrong that everything has a PLL.

The maximum system clock is not always needed, or can't be used. 

There might be restrictions on power usage where for example batteries would drain too fast.

There might be restrictions on available supply voltage, so with the available supply voltage, the system will work but maximum frequency cannot be reached.

Sometimes, a certain peripheral might need a specific clock to communicate at right speed with other devices with minimal deviation from the nominal speed. For example an AVR MCU running at 2 MHz clock can't communicate at 115200 baud rate, but it can when using a slightly lower 1.8432 MHz clock.