To give a very basic example: its times can't do input capture. This means you have no easy way to do high-accuracy pulse time measurement. Compare the two datasheets, and the STM33's timers literally have orders of magnitude more features.

Only having two UARTs can be limiting - and PIO is a no-go if you want offloaded parity checking and flow control. The PIO doesn't have an easy external clock input. No CAN or Ethernet makes usage in larger systems tricky. There's no USB Type-C comms support. Its ADC is anemic (only 4 channels, with 36 io pins?). There are no analog comparators. It doesn't have capacitive touch sensing. There's no EEPROM.

None of them are direct dealbreakers and you can work around most of them using external hardware - but why would you want to do so if you could also grab a MCU which has it fully integrated already?