After spending some days with the agriculture system I would summarize it as flawed, but definitely not crap.
The trampling is... let's say a friend wanted to check my crops, hovered in with his jetpack, failed to aim properly as usual and wiped out 2 crop setups trying to land. But I think this has been mentioned often enough.
The other things that annoy me are for once that on some plants (e.g. Ferrum) you cannot tell whether it is fully grown or not, and for second the crossbreeding of plants is way too random. For example I setup a farm of melons and pumpkins crossbreeding, and in 5 setups not a single one produced either melons nor pumpkins. As far as I can tell there is no reproducible rule on what happens if you crossbreed two plants, you always get either the first or the second plant, or something completely random.
The general problem with Agriculture (as well as with the entire IC2 mod) is that nothing that you generate through the system is useful for anything, you just breed plants to breed more plants. There are some useful outcomes, but the time it takes to breed these into a reasonable shape is so huge, that you would have already masses of it if you created it the vanilla way. I would love to see some plants being able to create basic materials to make it an alternative for running around mining, or EU-creation plants as a literally green way of producing energy. Other ideas would be ladder-plants that if placed on the ground quickly grow into a ladder, or redstone sensitive plants that can be used as alternate circuit setups. Things that are useful and an alternative to the usual way of doing things, so you don't feel like you wasted days of your life and all you got was some flowers.