I'm considering raising the elevation for buildings by a tile. This should eliminate that problem and making other buildings appear taller.
As far as the pallette, map tiles and characters have their own. This was done in the NES to make characters pop out on the map.
What's that thing in the middle? It looks like a pile of bricks more than a building, other than that, I really like this piece.
Super NES on the other hand, here is that Pallette...segaretro.org/images/1/11/Master_System_Palette.png
fc01.deviantart.net/fs31/f/2008/221/3/c/the_NES_palette_by_erik_red.png NES Pallette
the NES had a pallete of 53 colors, 24 of which could be displayed at a time.
How many colors are in your pallette? If you're going for NES, you're going to want to limit it to eight colors, including black and white.
The hidden treasures and passages remind me of the towns in actual NES RPGs. Thanks for sharing.