There's a perfectly good reason to use Shinji as a guinea pig actually. Kubo can't use Hinamori because she would die from that attack cause she's weak(and her dying is pretty much out of the question, this is a typical shounen manga where 95% of good guys don't die, and considering she's almost died twice, he's not going to kill her off now), so if there's going to be a guinea pig to be used for the attack it'll have to be somebody who can withstand it, therefore a captain. If Komamura himself had taken that attack head on right from the start he himself probably wouldn't be in the best condition to fight, because as we've found out, that attack is very powerful. Shinji copping the attack at least allowed Komamura to somewhat learn of its nature, even then he still underestimated it. Of course there doesn't HAVE to be a guinea pig but at the same time her using it to blow up a bunch of buildings doesn't show anything worth seeing, but seeing it damage somebody of Shinji's caliber is. And it's out of the question to use Komamura as the guinea pig as Kubo would want them to start fighting on somewhat even terms.
In any case, so what Shinji got owned? Big deal, he'll come back and have his own fight later on where he doesn't get beat down so easy. Every Shinigami will get their time against the Quincy they are meant to fight. Plus, Shinji is too cocky when it comes to his Shikai, he's actually the perfect person to use as a guinea pig. He got a nice slice of humble pie.