The problem with the edges is a bit strange. The clock rates aren't very fast, but the semiconductor process used for the ARM is indeed quite fast. The result is that the edge rates coming out of the MCU are a lot faster than you would guess they would be. Spray is all edge rate related, so indeed you can get "stuff" all over the place with an ARM. For short traces - not an issue. Longer traces over a good ground plane - not an issue. Traces all over the place and no solid ground plane ... you will see noise here and there. The objective is to get the thermistors at least to the 12 bit level and (hopefully) get them better than that. Since there are ARM products on the market with 13 to 14 bit ENOB A//D's you would like to be compatible with them as well. You never know when Atmel might play catch up ....
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