I actually noticed this after finishing "Deus ex Machina(limsa lominsa)". I wanted to make a thread about it back then but figured that the lack of interest would make it pointless. But yes, there is a clear difference between the main storyline cutscenes and the GC/Dalamud ones.
I had so many issues with the main storyline cutscenes, that I even began to rant about it to my brother. I didn't mind the first cutscenes and seeing how my character was somewhat weak. Heck, it's the beginning of the game why should I mind. However as the story progressed, I got tired of seeing my character get knocked down/out over and over again.
And my biggest issue with the main storyline cutscenes...My Companion!
This was the issue that I ranted the most about. It annoyed me each and every time that she was doing all the talking and my character just looking left...right...left....right...between the people that were being interacted with. I remember the ifrit cutscene still clearly because of that. My companion doing all the talking while my character just stands there going all "......." and looking all o_o
Then came "Deus ex Machina" and I finally truely felt that my character shined how he was supposed to be. No more running away, no more getting knocked out. Instead he beat the living crap out of that machine while everyone was running away. I was a happy man lol.