I need some advice for my next visit to the ortho...?

I've been with my orthodontist for almost three years now, and it's come to the point where for the past year I've left every appointment pissed off. I have the "sapphire-crystal" braces, the clear ones. My teeth used to be extremely crooked, and now they are on the brink of straight beauty. However, I've noticed little things that are preventing them from becoming perfectly straight. When the ortho put on my braces, my top left lateral incisor was super crooked, so the brace on that tooth had to be put on crooked, and it's still on a little crooked. The brace on my top right cuspid is slightly higher than the one on the left. My orthodontist said that wearing rubber bands 24/7 (literally) from the top to bottom cuspid on both sides would just fix everything. I did just that, nothing improved except for my bite. I've asked him to just change these little things and he just shook his head and said "It's all about the rubber bands." Is this true? He looks at my teeth for literally 5 seconds and makes his decisions. Should I trust what he says and just wait it out? Or should I get my father involved...