I'm pretty sure that the lockouts related directly to your paragon or renegade rating. In ME1 you can spend skill points to unlock them, but in 2 and 3 they stay locked until you hit a certain level. Not sure what though-- I was probably a quarter renegade on this play through. I never had any paragon choices locked out save for the VERY very last one at the end (which doesn't effect much),, and I had about half of the renegade choices locked out.
What I want, is storylines/missions to be unlocked and available to certain levels of paragon or renegade, and for more choices that have lasting consequences.