Never tried Microsquirt, but I have a Megasquirt V1 2.2 on one of my cars. Pain in the ass to setup, but Megatune is super friendly when you get it all squared away. I don't know how much of a fan I would be using it on a bike though. I'm constantly fine tuning the thing, but I'm stupid picky about where I want my AF ratio to be. The timing curve I just set modestly so I don't have to worry about it, I have knock sensors monitoring the thing and I haven't ever had a problem, plugs come out great, low noise, and fantastic power and partial throttle.
I wont recommend it, but I wont stop you if it's what you want to do.