I like the JC story alright, but there are some pretty obvious weaknesses.
I think the main one is that while the Act I of all the classes are repetitive, the JC is the worst offender. Sure, everyone has the same general thing, and each planet has a twist and fallout to deal with, and usually ends with a big moral, character-defining decision. For the JC, that big decision is always the same - to shield or to kill. Moral decisions help me color my characters - give them nuances that make them more interesting. So not only is the story more boring because you're always being confronted by the exact same decision, your character is more boring as well.
I think this encapsulates what I find maddening about this critique of the JC story. In absolutely no case is the decision solely about whether to kill or shield the master. Throughout the JC quests on Taris, Nar Shaddaa, Tatooine and Alderaan, while the ultimate decision is what to do about the master at issue, how you get there can be different. For example, on Alderaan:
That said, everyone is entitled to look at the story differently and I appreciate your comments.