The Rune Factory series is probably one of the stronger contenders for the farm crown. A lot of it is built into Stardew Valley after all, including monster ranching and the mine acting as a sort of dungeon.
The Rune Factory games are also quite charming, though one could argue the series didn't really come into its own until Rune Factory 4 with its expanded story, more interesting character roster, and excellent localization.
Where Rune Factory fails against Stardew is in how the former deals with the farming mechanic, particularly in RF4.
The Rune Factory games aren't about runes or factories. They're about upgrading as much as possible — your gear, your farms, your relationships, and your crops and soil, but not your own farming or growing abilities.
Growing quality crops in Stardew is part RNG and part planning. Fertilize the soil, and you'll get some good returns, if you're lucky. Over time, you can expand your operations as you take back your farm from nature and plan everything the way you want. It's your corner of the world to do with as you see fit.
Rune Factory has you upgrade crop levels so they're consistently worth more, and there's even a Giantizer to help ensure giant crops more often. It fits the series' fantasy theme, and it frees up time to do other things, sure.
However, it takes away some of the charm and satisfaction of seeing those gold star melons pile up in your inventory or waking up one morning to find a giant turnip peeking in your window.
That's because Rune Factory isn't really about that kind of satisfaction.
Farming is one of many activities, but after a short while, it clearly takes a backseat to other tasks, like relationship building or exploration, most of which doesn't rely on slowly creating a viable, vibrant farm. Shoot, you can even get a monster army to do everything for you, a lot earlier than you can recruit Junimos in Stardew.
In short, Stardew puts the farming first and lets everything else grow as a natural offshoot from that. Rune Factory has its place, but not necessarily as a top farming sim game.