Yes, much like the shortcomings of Windows 95 that spawned a million Notepad clones in the form of IDEs, code-oriented editors, and Office (née Works?)-like suites.
the notepad clones didn't require a storage engine. they saved files using the OS storage API
It can't handle anything resembling a large note, and can't link to other notes meaningfully.
Apple Notes has sync issues with large collections, and backing up to anything except iCloud is a pain.
I mean the obvious one is cross platform support? People who don't want or have an icloud account?
Contrary to your belief there are still people out there living outside the apple bubble.