I think the main story shouldn't have had the filler. The main story tends to bring you to various towns/regions where there are sidequests your level anyway, so we didn't need so many MAIN story quests to level 1-50 with main story quests exclusively. I'd have preferred if say... we had a main quest every couple levels, like with job/class quests, and for those who need the EXP, there's the local sidequests, dungeons, etc. The filler BS really dragged down the quality of the story too. But its too late to change any of that now.
Personally though, I don't really see the diff between having main story quests and side quests. Just skip the cutscenes if you don't like them.