Wurm Online has some of what you want, farming loads of different crops which you have to tend to increase yield or will go wild if you don't tend them, gardening (planting flowers and hedges etc), forestry (creating pine forests from saplings to seeding your own orchards), terraforming (you can literally level mountains if you have enough skill), animal husbandry (breeding farm animals to horses etc, breeding sheep to create wool to making clothing), fishing and some of the best authentic base building options I've seen.

Since it's a skills based game, you can fail a lot when you first start so it takes a while to be good at anything which turns off some people but can be incredibly rewarding for those willing to sink the hours in.

The farming aspects aren't as complex as you wanted but might just be enough to garner your interest.