I'm automated a great deal around my house with Arduino trying to get used to it (my curtain controller stepper motor broke this morning :() and in doing so have bought far too many Pro Minis. So I've designed a PCI card with an ATMega 2560 on it and all the leads on the backplate. I've got 3 UARTs spare, 40 IOs, 12 PWM, 16 analogue ins and a direct FTDI into the computer.
It's not particularly hard to take the 2560 reference design and make it fit a PCI board although the PCI custom part is slightly annoying. I'm waiting on its arrival to get my server hooked up and take over everything in the house :D
Also you may want to consider doing sensor boards instead of just sensors. That way calibration is done by the board and the output is exactly as you wish so your Atom only has to interpret lightening its load.