well, first thoughts - it's a good idea, I'm looking at an NXP ARM device for a new board design, but I'll throw my criticisms in as well:
Your cap's near the pins will affect your sample times on the analogue reads - as for thermistor sensor reading, they have a specific source current that should not be exceeded, this is usually a part of the design of the circuit that reads the thermistor
You've tried to address the max voltage issue, but I would suggest being aware that some pads are voltage tolerant, and others aren't, so you may find that there's some that you can use specifically for high voltage tolerance (12V) and others where a voltage divider will do for input (and a BJT for output?)
EMF is a whole lot of black magic, I've had fun designing my own power supply (1A 5V Buck converter with a 9-30V input range) to filter out the unwanted noise, and it's the noisy components that need EMF protection (solenoids, switches, motors), or you need physical design to protect from it (farady cage around your board to remove it's susceptibility to EMF - think metallic powder in the plastic case)
noise protection on input lines is a fine art, and pointless if you shield the cable but do nothing about the rest of the electronics. Usually you connect one end to an earth and leave the other end hanging (or even disconnect both ends and have a central bond point for the shield), any other way and it acts more like a wave guide, transmitting noise from one side (that noisy coil in the PC power supply) to the other (your nicely shielded box housing your electronics) - ground loops in shields are an extension of the same, don't eliminate them (impossible) but try to make them as short as possible and as far away from the sensitive stuff as possible.
Your cap's near the pins will affect your sample times on the analogue reads - as for thermistor sensor reading, they have a specific source current that should not be exceeded, this is usually a part of the design of the circuit that reads the thermistor
You've tried to address the max voltage issue, but I would suggest being aware that some pads are voltage tolerant, and others aren't, so you may find that there's some that you can use specifically for high voltage tolerance (12V) and others where a voltage divider will do for input (and a BJT for output?)
EMF is a whole lot of black magic, I've had fun designing my own power supply (1A 5V Buck converter with a 9-30V input range) to filter out the unwanted noise, and it's the noisy components that need EMF protection (solenoids, switches, motors), or you need physical design to protect from it (farady cage around your board to remove it's susceptibility to EMF - think metallic powder in the plastic case)
noise protection on input lines is a fine art, and pointless if you shield the cable but do nothing about the rest of the electronics. Usually you connect one end to an earth and leave the other end hanging (or even disconnect both ends and have a central bond point for the shield), any other way and it acts more like a wave guide, transmitting noise from one side (that noisy coil in the PC power supply) to the other (your nicely shielded box housing your electronics) - ground loops in shields are an extension of the same, don't eliminate them (impossible) but try to make them as short as possible and as far away from the sensitive stuff as possible.