Yup, I missed tons of optional missions too. ME1 requires you to walk around everywhere all the time to find every mission. ME2 has less of that, you'll find side missions pretty easily.
I remapped all the controls back to the ME1 layout because of that. Of course doing that renders all the help tips useless.I have Mass Effect 2 waiting for me now. I started it up and played the first few missions, but the change of controls keeps confusing me.