Clearly the goal of Prophecy was to make Casey the new 'player character'. As cringe-inducing as it was to have a senior officer humbled by a rookie pilot in such a manner, it's to help build Casey's story and character for the player. Given the flickers of maturity we saw in WC4 (particularly his dismay at observing the Intrepid's damage when he firsts arrives), it does seem a missed opportunity that Maniac is reduced to comic status in Prophecy. On the other hand, there were plenty of times he was treated as such in WC3 and WC4 too (eg Hawk/Panther's reaction to Maniac's antics), so it could be argued Prophecy was just a continuation of that.
Edit: From a story-telling perspective, I suppose there is some merit to teaching someone the goodness in responding with grace in the face of hardship such as bullying. The execution in Prophecy might not have worked that well, but I appreciate what I think is the intent in that teaching, in having Casey rescue the pilot when Maniac wasn't able to. Remember the CAG explicitly ordered him on another mission so he couldn't do so himself. (Okay, so Casey was rather snide in announcing to Maniac that he was going to make the rescue attempt, that wasn't very gracious, I know.)