Some modern embedded graphics hardware does support palette textures in the TMU. It's more a specific implementation detail though, as you've mentioned, because it's doable in the shader.
Without my ImgTec hat on, mobile embedded graphics isn't a mess just because of the extension mechanism, but also because embedded graphics is still taking some fairly baby steps and there are
many more players in the market.
Khronos doesn't have the ability to force all of those vendors to spend area on features, so chances are anything expensive isn't mandatory in core, but is optional via extension. Unless the market gets smaller, getting a concensus on core features is going to be difficult, and the Khronos voting mechanism has some inherent problems when trying to achieve that.
sebbbi's concerns are almost completely valid, when it comes to having to add branches to your code to support myriad different HW platforms because of that.
It's just because the market is immature and filled with players. FWIW (ImgTec hat back on), we put emphasis on shipping a stable, compliant driver with support for lots of extensions that are helpful for developers. However, we can't force our customers to ship the extensions.
There's no easy way for sebbbi to get what he wants. The best place to start is Apple, though, to get them to ship more extensions for GLES2. Drop our devtech team a line and we can pass things on to Apple, or you can get in touch with them directly and make the case. Good luck getting ETC though