IMO only, I would have placed Anna Rchnio and Elena Liashenko ahead of Michelle on that day. Lastly, I would have placed future OGM Sarah Hughes ahead of Michelle. She definitely flutzed however, she landed a nice triple flip which was more difficult than Michelle's 3 Toe and she had better spins than Michelle that day.
Hughes underrotated her Flip, so I don't consider that jump she did to be better than a 3Toe. Her jump combo was barely rotated on both of the jumps and badly flutzed, so even with Michelle's fall on the 2Axel, Hughes really isn't that far ahead in total on the jumps to me (I'd have a .2 separation between them on the tech mark for jump elements). Her layback was better, and the flying spin had a bit more to it, but I wouldn't call her combo spin better. The footwork sequence and spiral sequence were both inferior to Kwan's; in total I would have Hughes behind Kwan by .1 on the non-jump elements, which puts Hughes' final tech mark ahead of Kwan by only .1, not much of a cushion. Kwan was far better than Hughes in all regards on "the second mark", especially since Hughes ended her program way after the music, so it's really not close to me.
Rechnio I can understand placing ahead but there were actually a lot of problems in that SP. No required footwork at all into her Flip was a big one. I guess it comes down to how much you liked her presentation; for me she rushed through it too much and didn't have any particularly great moves. Liashenko is the same situation, many tech problems with her performance even if "looks" relatively clean, and some strong aspects to her skating but also notable flaws - not much stretch, awkward jump entraces.
That SP competition shows a potential benefit of CoP scoring - there wasn't a huge difference in overall accomplishment between the programs, so certain people getting buried in the SP placements isn't an accurate reflection what everyone actually did. In the end Michelle was definitely 2nd best in the LP by a pretty big margin, so her Silver medal was correct.
There's a huge difference between thinking a skater should have won a competition and thinking that the only explanation for a skater losing is due to bias. Both Michelle and Irina did things better than the other so, when both are clean, either could win.
Irina's programs were almost always far below Michelle's in terms of performance/choreography/interpretation, certainly that was the case with Irina's Tosca. She had bigger jumps, but that alone isn't enough to make up for her other deficits. If they are doing the exact same jumps in a program, then there's really no way Irina should win. She should only be able to win if she does more jumps than Michelle...and even then, not always. There wasn't much going on in her skating. Mainly just jumps, speed, and sometimes a good spin.