Well the idea is to have somewhat of a large, unified (or bifid, since you want NES-ish and SNES-ish sets) tileset, is it not? If two people make a "red" enemy with completely different palettes they can't both use cset 8 - at least not in the same quest (until 2.54 comes along, but you'd need a script which is no good for newbies). If there's a common cset structure, if not a common palette, then at least it's easier to make them work together.
While that 'would be nice', a single unified palette just does not work. I have tried this, in two quests, and it became a handicap, and a liability.
Designing the modules to use palette changing is critical. The target for these modules is 2.55, so, designing them will need to move to 2.54 after some of the basic stuff is ready; and default scripts will be provided in them, and set up in a way that allows using editor components to define them, quite easily. I've spent a lot of time ensuring that many of the core scripted components will be something that the user can edit from the editor, without ever needing to know how the script functions.
(This is somewhat of a hybrid between the base ZC philosophy, and the philosophy of Solarus; and it is what I suggested for Solarus as well, which seems to now be a goal for Christopho. In any event, scripted engine effects, and events, need never be visible to the end-user...)
(There's an awful lot of automation planned for this stuff.)
If you can suggest palette structures though, I am certainly not opposed to any of them. It's up to the entrants to decide how they want to organise stuff, but in general, i want to see these modules as easy to use, and using ZC features, wherever possible. Designing palettes to use the ZC palete structure is proba bly the best way to go, and SNEs graphics that use this format should work, as long as the level, sprite, and boss palettes are all designed to use the core features.
Zelda 3, as an example, loaded alternate palettes for the dark world, and most dungeons.
For a unified palette, scripted control would be the way to go. Load a completely custom palette at any time, changing every VSet to whatever colour swatches you want.
Otherwise, you are extremely limited to colour choices, and need to design all of your tiles in 8-bit. For these entries, tiles should be 4-colour (for NES, and Gameboy--although 16-colour is allowed for a 'Super Gameboy' entry, as that system could use SNES gfx)) and 16-colour (for SNES). I would prefer that 8-bit stuff be used only where absolutely needed.
I also prefer that tilesets are designed with both layering, and combo aliases, in mind; so that laying down screens becomes easier, and the need for tile/combo modification is mitigated.