I think you're conflating two things here. I imagine what you hate is using proprietary software to upload arbitrary files when you feel like you ought to be able to use your OS's built-in file copy mechanism.

However, there is no reason that these file transfer protocols cannot appear to the user as a standard filesystem. There's little similarity between FAT, NTFS, ISO-9660, UDF, SMB, etc., yet they all appear to the user to be more-or-less the same. And all modern OSes are extensible to add more file system types, and there's no reason that MTP cannot be implemented as one. In fact, there is a filesystem metadriver called FUSE that works under Linux and MacOSX (amongst some other Unix-like OSes) and there are MTP implementations for it.

I have no idea what the MTP experience on Windows is, but I kind of suspect that it's worse than what it will be under MacOS and Linux, because it's less likely that anyone will bother writing an IFS driver for Windows if it's built in, even if it is only as a separate interface.