better get the Arduino Mega coz it has more I/O connections
One thing to remember though is that your sensors and actuators will be placed over a very large area, IMO it's not practical with many such devices to have long cable runs back to a central uC. Too much noise, voltage drop, ESD potential etc.
For this reason I would suggest distributing your processing, and that means a network of some kind. It can be something simple based on RS-485 or similar.
As for the various Mega options, I'll let someone with more Arduino knowledge answer that.
Rob