Junpei's reaction to having superpowers is a lot more realistic, I think. I mean, to start off, he was a loser, let's be honest. And how would any loser react to superpowers? They'd be ecstatic, they'd feel validated by the world, and he does. But then he begins to wonder, what does that mean? If his power is all that gives him self-worth, is he really any better off than before he discovered it? Is he possibly even worse off, because now he's not only a loser, he's also a poser hiding behind these superpowers he did nothing to earn and can claim no credit for? And then, it gets even better - they all find out that their power is a means to its own end. If they end up using it for its stated purpose, to defeat the shadows, they will end up eliminating their own powers in the process. So to use his power will mean losing his own power and returning back to being normal, i.e. a loser. The relevation throws him for a loop, and he pretty much loses it - mouthing off to the main character, lying and pretending to be the boss; his insecurities come foaming to the surface.
In the end, he finds what is right in his heart through a number of reasons, primarily Chidori's love (but I think his teammates and his own sense of responsibility help too). His development as a character is among the most convincing and touching I have ever seen in a videogame.
As an aside, I also love how subtly his development is displayed. Most of what I wrote is never explicitly stated in the game, but he is such a well-written character that you can just tell how he feels and what's driving him. It's the little things - the tone of voice in some of his lines, the change in battle quotes - that make his character work.