Yes, the Arduino is well suited. Any of the boards will work. Unless you have a large number of sensors, or are not planning on using a serial LCD, you do not need a Mega.
The Duemilanove and Pro are different form factors, not different chips, so the choice depends on what you are comfortable with. If you want to plug in, and unplug stuff, the Duemilanove is the way to go. If you want to solder stuff to the board, get the Pro.
USB is a data transfer protocol, not a file storage medium, by the way.