You can hardly compare the atmega series CPUs with 32-bit ARM SoCs running at 10+ times the clock speed, much more memory, and many more advanced features. The RP2040 (the SoC on the pico) is very much a generation beyond the atmegas, if not more.
Notably the PIO feature on the RP2040 is used to avoid having to sample input pins using the ARM CPU (which would make it slow and undeterministic). The sampling is effectively hardware-assisted using the PIO feature. The github page in the link goes into some detail about it.
I'm asking for them to be compared in terms of IO features, not absolute performance. The ATMega has it's own range of hardware driven input features and that's specifically what I'm asking for a comparison to.
Not really sure what you mean by i/o features, but I generally don't get why people don't look up the specifications if they have questions like that. They do exist for a reason.
Notably the PIO feature on the RP2040 is used to avoid having to sample input pins using the ARM CPU (which would make it slow and undeterministic). The sampling is effectively hardware-assisted using the PIO feature. The github page in the link goes into some detail about it.