Well there actually is a third solution: incorporate the filter housing in the air scoop, so you'll have filtration and enough airflow when the car is driven, and uncovered, shiny stacks when you open the hood.
Look at this picture from the CC galleries:
However this will only work for straight stacks.
James, why do you want to replace the Megasquirt? I'm having a stack injection setup here waiting to be installed, and I planned on using the Megasquirt as it seems cost effective and user friendly.
Simon