It's funny how more people seem to say that without even trying it.
I've built several now. But compared to MFR or SC2 farms they've never been worth the effort or resource investment. They also seem to flip out after server resets. On more than one occasion I've found them in a state where I had to put down a block next to them to wake them up. But most importantly, they feel boring to me.
But either way, you can snark all you want about how no one tries them. No one really
wants except when Forestry demands they do it. Even Direwolf20 seems reluctant to engage in them because Golem farms are so dang much better. He has one and he, one of the better large-build guys you can ask to meet, found them difficult and poorly documented. So, ah... I am glad they work for you. I submit they need design work.
It was the reason crop rotation system revolutionized farming.
I got no problem with fertilizer so long as I have SOME process to make that automated. MFR's system is really clever in my opinion. You need plant farms to help with animals and animal farms to help with plants. Seems good to me.
MFR's design is superior because you can engage with it and disengage with it at will and expect to to continue on relatively well. Forestry's system isn't "stable" in the sense that it requires constant human intervention. Look at most of the successful and popular solutions in Minecraft; people "build something" and then it works forever and they start working on the next project.
This is why Bees are great, trees are not awful I guess, and the farms suck. The farms require you to baby them forever, wheres bees or a properly built boiler system do not. You will be forever going back to an unsolved project because Apatite is just not common and requires unique mining. You can say that's more realistic, I suppose, but that's besdies the point. People play Minecraft to escape into lego projects, and part of the fun of Minecraft is the sense of completion.
Torches don't go out, right? Because that'd be tedious. Same principle.
In an actual tree farm, you cut down the trees when they mature, you plow up the dirt, re-fertilize it, then replant. So seems fairly realistic to me.
Please note above where you pointed out Minecraft is not realistic. It shouldn't be without a total mod conversion like TerraFirmaCraft.