I wouldn't go so far as to say he had "no business" applying. I have watched him in a few CSSHL midget games this year and a few Ice games. He is not a flash player like McDavid, but he is very smart, economical and effective. Keep in mind that his place in the bottom six on the Ice depth chart is likely a result of him being restricted in the number of games he can dress. If he was a regular player, he likely would be in the top 6. In the CHL, if your not in the top six, its awfully tough to produce.
I have to admit I'm a bit of a CHL novice but I was always under the impression that exceptional player status was not meant for any underage players who could manage to crack a CHL roster, but for guys who were fully prepared to get in there and play full time on a top line, that sort of thing. Basically like McDavid. The WHL decided he didn't quite measure up to that standard and with the greatest of respect for Savoie because he's clearly going places, I can't say I disagree. The incident where he was concussed on a hard but clean hit by a Brandon player in December was an illustration of that. Just the lack of refined instincts when playing against guys much bigger and stronger than you. That said, I might have felt differently if the Ice didn't have so much depth... they can afford to wait for Savoie.
I'm fine with him getting a few games in just to get a taste of what's next, but I'm not sure I'd put him over Isaac Johnson or Michal Teply at RW on the depth chart.
I have definitely noticed what you're saying about the bottom lines in the CHL, though. Some of those guys are barely ever on the scoresheet. The disparity between top and bottom lines seems wider than with the NHL. I've never seen TOI stats for junior but they must be minimal for the 4th line and 3rd D pair, although Savoie did get at least a bit of time out there.