All of the 55 I/O pins should support ADC and DAC? No way. There are 2 DAC channels, and maybe a dozen ADC on STM32 MCUs/MPUs. Use external ADC/DAC parts connected to the SPI bus.
Otherwise check out the STM32MP1 series.
"Best" is a subjective term.
I do not think any of the stm32 microcontrollers will run linux, but the STM32MP1 will.
There are such things as "IO Expanders" chips that connect over I2C or SPI and provide 8, 16 or more I/O lines. I used to like MAX6956 because you could control the brightness of LEDs without having to resort to PWM, and newer ones of these have built-in PWM for the brightness.
But unless you expand on how you intend to use all those GPIO lines, it is hard to advise further.
You might be better off with one of the commercial Cortex A series boards built around an A7 or better multi-core application processor, rather than an eval board. There are quite a few sources for these if you do a search. They will have a BSP already configured for the board and better support than what you'll get with ST Cube software.
Or latches/buffers banked on the external bus (FSMC/FMC) to provide parallel access. Also attachment of things through a CPLD which would manage high rate interactions on the pin whilst decimating loading on the processor for interrupts, etc.
Trade-offs in size/cost, pin escape and desire to use LQFP vs BGA