Or rather we should get rid of the 4 bit limit.
Now obviously we can't get rid of per-sprite indexed-into-master palettes, because both palette swaps and master palette modifications (ie. single shared master palette) need to continue to work. So making sprite palettes bigger than 16 colours (up to 256) is a natural extension.
If you're using a (copy of the) 256 colour sprite palette that just maps straight to the master palette, then the sprite editor can just pretend that you're using the master palette directly. Otherwise, having one 256 colour palette mapping into another is rather messy (and you surely don't want them both onscreen at once). Sprite palettes should probably be variable length rather than length 256.
Unfortunately remapping huge palettes would also be way too much work without some special tools. There's an alternative, see below.
I guess we'll have to wait and see how well it works in practice.
Newbie Newtype wrote: for pixel art 256 colors is quite enough, and you can have multiple master palettes now
Well the problem is, you can't really use them. Being able to use multiple master palettes at once would be quite nice. It would allow lots of stuff like fading out the whole screen except for some object(s) or a text box (requested many times), and using a different palette for error messages or the UI in Custom. Custom would probably be much more colourful.
That requires switching from 8-bit to 32-bit colour display internally (bonus: alpha transparency), which Jay has actually already put a whole lot of work into.