When you take out the first big chunk, it won't all be all the same layer mostly because you will be using a steep angle to remove it. After the majority of the material is removed, I switched to a smaller 1/2" chisel (I used a 1" to remove the large portion) and tried to lay the chisel as flat as possible. To control the depth, you will have to periodically stop and check your depth with a gage or small block of wood that is the same thickness that you are trying to recess. When you have the area you are working on the proper depth, you can move to the other areas and pretty much just "pop" the remaining material out by keeping the chisel flush with the area you just completed.
The thing with MDF is that because it is layered, you can keep peeling it back and it will keep getting deeper. Like trying to pull a sticker off a cardboard box, sometimes the more you peel, the more cardboard comes off with it, if you follow me. This is why your chisels have to be sharp, cause then you can control this peeling because the chisel will cut the MDF rather than let it progressively peel deeper.
This sure does sound like a lot of work when it's typed all out, but it honestly only took about 15 minutes to do that one joystick in the picture. When complete, the recess I did turned out level. It really isn't hard to control the depth on MDF. I wouldn't even try using a chisel with particle board, though.