Not the pixel art style that you seem to mean but there is a recent lemmings 3D style game called Tin Harts. I haven't played it yet but it looks interesting.
Also, it is voxels rather than hand drawn pixel art but I thought Urbek did a great job at feeling like that era of game. It is as much a puzzle game as a builder (there are a number of levels of upgrade that require other buildings within a certain distance).
https://www.gog.com/en/game/tin_hearts
Also, it is voxels rather than hand drawn pixel art but I thought Urbek did a great job at feeling like that era of game. It is as much a puzzle game as a builder (there are a number of levels of upgrade that require other buildings within a certain distance).
https://www.gog.com/en/game/urbek_city_builder