The comparison to Jordan is interesting, but Jordan was always the hands-down best player on his team, even when the Bulls were lousy. Bryant has had to mature in O'Neal's shadow, and that's something Jordan never had to deal with.
And frankly, if I were a superstar but the second option behind O'Neal, I'd probably be griping a bit too. O'Neal doesn't bring his best effort every night. I've watched the Lakers a lot this year, and Malone (pre-injury) ran circles around O'Neal in terms of on-court energy. O'Neal seems content, at least so far, to take a back seat to the new stars and let them do most of the work. Of course the Lakers are struggling now with O'Neal and Malone both hurt, but in fact they were already looking mediocre when it was only Malone who was missing.
Meanwhile, Bryant -- who, in spite of his personal problems, can hardly be accused of bringing subpar effort to the basketball court -- has to hear over and over about how the Lakers are O'Neal's team. He is forced to fall in line behind a "leader" who doesn't reliably lead. When the Lakers struggle, it's because O'Neal is out of shape, or hurting, or bored, or sulking over his contract, or whatever. And Bryant has to sit there and take it, even while his own effort is much more consistent.
This year is different because of the rape trial, but in my opinion the Lakers would be better off if Bryant emerged as the leader now. O'Neal may be more dominant, but he no longer has a leader's mentality.