Fighting "phantom Nicole" and "The Marker" is not so bad. It's just getting there that's the hassle! That and you have to do one more difficult qte before the boss battle but luckily there's a check point right before it.
As for Birth By Sleep? I love it! It has flaws (like empty environments) but I find the gameplay and story telling to be very good. (If not a bit resemblant of Star Wars)