Off the top of my head,
- installing applications that aren't available as flatpaks requires you to use distrobox to install them (not a huge issue if you're familiar with the terminal).
- printer drivers are very difficult to install if your printer isn't supported out if the box, as they cannot be installed in a distrobox container.
- changing user groups or permissions, such as to enable ssh or ftp abilities, is more difficult (it wouldn't retain the setting after rebooting, didn't research how it can be achieved).
- not a limitation, but it's much slower in many ways compared to normal distros. It takes a long time for it to finish installing, booting is slower, updating is slower, etc.
There may be more limitations, but those are the ones I personally encountered.
Then I would suggest the standard Linux Mint Cinnamon, which as I said makes it extremely easy to install the Nvidia driver.