Minecraft has redstone, and redstone torches, which basically gives you electricity, electric power sources, and easy-to-build transistors. This makes certain computational functions a lot easier, since you don't need to mess around with pumps and pressure plates and mechanical power. You can just build logic gates directly. On the other hand, you're limited to on/off digital signals only. The way mechanical power works in Dwarf Fortress makes it possible to hold and compare analog values, which is how I'm doing the "greater than four neighbors/less than two neighbors" checks with only a handful of gears. I expect that the DF mechanism takes up a lot less space than the equivalent Minecraft circuit for this function.
The main disadvantage I have seen in Minecraft (and I haven't played it yet, just read through tutorials and watched videos, so take this with a grain of salt) is that electric signals need a continuous path of redstone dust to travel through, and have a limited propagation distance before needing a redstone torch to boost the signal. You can't link a single gate to hundreds of triggers all over the map with invisible, instantaneous circuit connections the way you can with mechanisms in DF. In DF I can link a single pressure plate to hundreds of gears, doors, hatches, and other buildings all over the map, with the links taking up no space in the design, and have all the devices respond instantly when the trigger activates. I expect this to be the main limitation on making really large, complex computational engines in Minecraft.