This may get long winded. I apologize in advance.
JC was my first class to 50, and in the time since, I've gotten a SW and IA to 50. I duoed the JC with a JK all the way up, so I have seen the vast majority of that story as well, barring a few CS that don't play (holocalls, etc). I can safely say of those four, the JC was easily the weakest story for me. There are several, several reasons, and I tend to ramble all day when this is brought up. I'll try to keep it concise.
Act 1: I actually enjoyed the premise of this act moreso than the following two. What completely gutted it, however, was the fact that choosing to shield each master had zero consequence whatsoever. Your companions and others keep impressing on you how this is risky and you could easily kill yourself but absolutely nothing happens.
As mentioned by someone else earlier in the thread, if they'd even done a temporary thing like Voss, that would have been something, but they didn't. I never had any kind of weakness or consequence as a result of my choice to save these masters, ostensibly with my own life force. This is supposed to be a unique, rare power, and yet the consequences weren't just glossed over, they were largely ignored other than lip service. Except for Voss. I appreciated that, but then again Voss is good on every character I've had at that point so far. There should have been some kind of consequence, and that alone might have solidified Act 1, at the very least, as a good plot.
Er, Persona 3 spoiler ahead, doubt anyone cares but:
The Rift Alliance: I didn't care about them at all. I'm completely serious. The only people I really cared about was Nadia and her father, and the outcome of that little arc was moving somewhat. The rest of them, I can't even remember their names, or what they wanted. The only impression I can remember lingering to now was that for the most part they were typically whiny political types and I wanted to airlock them. (Thank you, President Roslyn for making airlock a verb. <3)
The Emperor's Children: This was another plot thread that had potential, but fell flat for me somehow. The twist I kind of saw coming, unfortunately, which probably deflated it a bit for me. But aside from that, each of them, I suppose I was meant to feel some kind of pity for, or something, but mostly I just didn't. Again. I can't really offer a solid logic behind why for this particular instance, so I can understand if you dismiss this particular reason as trifling.
Duoing with a JK all the way to 50 certainly didn't help me, as I found what was going on in his story infinitely more riveting than my own, which only served to magnify my boredom, I believe. Personally, in a story, I like to have my characters go through some really rough patches, often with bad things happening to them. If there are never any real dire consequences in a story (or ones only mentioned and never seen) it tends to come out feeling flat overall to me. I suppose I like the 'trial by fire' thing.
Last, the romances. To be frank I'm not that into the LIs for nearly any of the female classes, but the JC has probably some of the least interesting. Tharan is the type of 'charmer' that is actually more irritating than not to me, and that doesn't go anywhere, regardless. Iresso really didn't intrigue me much, either. Zenith would have made an actual interesting romance, but was sadly unavailable.
Long story short: Had Act 1 had the consequences they kept harping on, I would probably rank the overall JC story somewhat better than I currently do. As is, it's definitely at the bottom of the list of the ones I've finished/seen finished so far.