It's still relatively uncommon, whereas it could indeed be useful in some cases.
A couple notes about that:
* Many modern MCUs do have a relatively wide operating range for Vdd - often between 1.8V and 3.6V. That doesn't give you multiple IO banks, but you can certainly use 1.8V logic without any external level shifter. In that case, you still can't mix with 3.3V logic directly, but can still be useful. Just mentioning that because a lot of people don't think about running their MCUs at lower voltages than 3.3V, even when that would make sense! (And the additional benefit is a lower power consumption.)
* Also on a growing number of them, you have a separate voltage rail for the core, thus powering IOs at 1.8V doesn't hinder the max frequency at which you can run the core, which OTOH can be the case on some MCUs.
* Same for FPGAs, but worth noting: a typical voltage range for IOs of 1.8V to 3.6V is no big problem, but if you wanted anything above the (typical) 4V absolute maximum, that will usually require using different CMOS processes, and be (much) more expensive. So don't expect such devices with a range up to 5V or higher, except niche, expensive ones. "5V-tolerance" is easier - but that just means inputs can take up to 5V, while the IOs are still powered at lower voltages. That's not quite the same, there's no level shifting in this case. Now there's still some MCUs available with a 1.8V to 5.5V voltage range - often 8-bitters or a few entry-level Cortex-M0 ones - but those are usually on "older" CMOS processes that have lower density, so not adapted to more complex and higher speed devices.
But apart from the two examples mentioned by some above, I don't have others in mind.
You can also typically find this on processors taking DDR/2/3 RAM, which have a separate voltage rail for the RAM interface - but then those are IOs that are reserved for DDR RAM, and not GPIOs. And those aren't MCUs per se - at least I don't know of any "MCU" taking DDR RAM as of yet. Maybe there is? But the families that are often called "crossover" these days still support only SDRAM. AFAIK.