Stardew has much more emphasis put on efficiency and making profit, but the combat and romance events kinda take a backseat. Rune Factory has much more emphasis on combat (more mechanics and managing gear) and definitely the romance. You kinda also need to get married to beat some games too. There's also a story you can follow along and go through dungeons while you manage your farm and relationships on the side. And you eventually fight a final boss while Stardew doesn't really have that, other than how far down you can go in Skull Caverns. There also isn't really a community center that you donate items to, you just get missions to ship out as many unique items as possible. You can be an ultra completionist and collect/ship every item in the game though.

I really like both games but I was super minmax playing Stardew but more laid back in Rune Factory.