I have two primary concerns with the new forestry farms, one is the apatite input required for _everything_, and two is the general space required.
The space requirement, for everything but the tree farm, has shot up tremendously. Old wheat farms held over 120 growing spaces in a 15x15 area. The new farms either match that in a slightly smaller space, or beat it slightly in a larger space. But only if you ignore the vertical. Old wheat farms, peat farms, etc, had a height requirement of only two blocks. The farm itself and some air. The new farms require 4 blocks high. So before, where you had 240 growing spaces, you now have just 120, or 156 if you go with 15x17
(I also suspect, but haven't tested, like most multiblock structures, that they need a block between the farms vertically, so really the farms are going to require 5 blocks high in order to stack them)
The apatite requirement isn't itself crippling, except in the face of other methodologies available (turtle and steve's carts for trees, golems for wheat/carrot/potato/netherwart, any number of methodologies, some even vanilla, for cactus, reeds and melons. Basically it's a maintenance requirement that I want to avoid - and I have the option to do so by going a different path. Trees grow on normal dirt, after all.
Ignoring build-cost, I'll personally be switching away from Forestry farms solely due to the mining input required of apatite. Humus was bad enough when it didn't require apatite, trees grow on normal soil, the creation of a humus was an unnecessary requirement.