The problem with micro-controllers is their sensitivity to RF noise. I was using an Arduino board under a florescent desk lamp and it kept locking up which I had never seen before. I initially thought that I had cooked the board somehow. With the desk light off it worked just fine.
I test automotive ignition systems and they generate quite a bit of RF noise, can't say I surprised that they had trouble running a MC next to an ignition coil.
With the new Coil on plug setups you can get the coil far away from the controller and it should be easier to implement. Add some RF filtering and maybe an opto-isolator and it should be just about bullet proof.
I've got a "homebrew" CDI setup that I'm testing now using a standard magnetic pickup instead of a hall switch. I find the halls are too sensitive.