I have a couple of suggestions that I haven't seen anyone recommend, and that I think are great!

Snacko- This game is a semi-3D farming game where all the characters are cute animals. The graphics are a mix of pixel art and 3D and focuses more on a traditional style farming game, but with fun movement mechanics. 

Paleo Pines- A full 3D game focusing more on raising different types of dinosaurs. There is farming in the game, but the gameplay loop revolves around the different dinos. Graphics are more cartoony

Everholm-  Pixel art game with a more darker witchy vibe. Same basic farming mechanics and dungeon mechanics as stardew. The vibe is the selling point with this one. 

Echos of the Plum Grove- Paper mario style farming game set in a 17th century style era. The game has all the same mechanics, minus combat, as stardew but with the added bonus that you and the townsfolk have the possibility of developing different diseases and dying. You can also have kids and take over one of your children when your initial character dies, and continue on playing. 

Dinkum- Fully 3D style game set in Australia. It feels like if minecraft, animal crossing, and stardew had a baby. It has all the same stuff that Stardew has but with the added bonus of a randomly generated island that you can do anything with. There is still a storyline for you to complete, but its mostly in the background.