It's all about muscle confusion. If you feel that you're getting a better burn from 1 or 2 shoulder exercises in phase 1 than the ones in phase 2, just replace the 2 exercises that you don't like the most in phase 2.
I don't even follow the the whole p90x program anymore. I take elements from p90x, p90x+, 10 minute trainer and other exercises that I know and make my own regimen.
Find what's best for you and do it