This looks lovely. The only thing that bugs me is the shore corners, with the chunks bitten out of them.
If you make this game use a 2nd overlay tile layer for those.
Oh that's a great idea! I was just going to make every possible combination of shoreline plus reef as their own unique tiles. Yuck!
Yeah man, looking really attractive. Surprisingly nice colors adaptation there.
Why use an overlay just for those tiles? I say a couple tiles are missing from yer collection. Specifically, 01, 03, 07 and 09.
Oh you number them the same way I do!

Also missing 15 and 16.

It's just that the Reef tile should be placeable on any water tile, so there needs to be a Reef variation for all 15 shore/water tiles. Better to just make it an overlay.
And yeah, I was actually kind of surprised myself. Much earlier on I toyed with doing a kind super-gameboy-style palette-swap for all the tiles. So swap out the second lightest grey for, say, green, for the bamboo forests, orange for the mountains, etc etc. It looked pretty awful, I really didn't like it. So when I decided again to "try it with colour" I was a bit skeptical.
I like my solution anyway. All the less time being in a map editor having to place corner tiles, and corner tiles tend to be very small and take up small portions of larger tiles, so it saves some space.
It's simple enough to make the map editor automatically generate the appropriate shorelines based upon where you place water and land.
Having said that, I did actually consider the method you've suggested before ptoing suggested overlays. I do see merit in it when more hardware restrictions apply.

Speaking of restrictions, they're basically thrown out the window at this point. I just put colours where I WANT now.

Little tiny update, just some stuff I did before I went to bed:

Worked on the castle, tweaked the grass colour, polished the small mountain tile.
In other news, I started... sort of... coding it? I got it loading a tileset and generating a random map. Small steps (I've never used lua before...)
More betterer updates to come!