Yeah, most of the palettes so far have just had darker shades of the exact same color for their darker bits (aside from the overworld's cset 4 which has the snowy white + teal-ish color setup, and some of the dungeon palettes which do have a bit of a shift for the lightest and darkest colors on the walls and doors.) I may fiddle with them a bit more before releasing the tileset, though.
I'd like to ask, is your example quest using any scripts? Since you obviously know how to use the Enemy Editor fairly well, I know a really easy script to use that lets you make 32x32 enemies through the Enemy Editor, if you'd like to have something other than the default bosses to use.
I haven't tried scripting in ZC at all yet, so at the moment there's no scripting involved. Also, as mentioned before, my sister is the one actually working on the example quest (and she's basically learning how to use ZC as she goes along; she seems to have a pretty good grasp of map setup, enemies, etc. but still needs a bit of help with setting up secrets and items occasionally)--I'm just making all the graphics and setting up the custom enemies. She has mentioned that there aren't many good boss choices among the default enemies, though.
I've actually tried making a bigger mini-boss sort of enemy once (and found that unfortunately the default "walking enemy" type only uses one tile of a 32x32 enemy sprite if you try to set it up to use something like the boulder/Aquamentus/etc. sprites), so a script that makes that possible through the enemy editor (without any need to program every little thing of the enemy in with scripting) sounds like it could be really useful.