There is not much solid analysis at
http://en.wikipedia.org/wiki/Quadruple_jump_controversy.
The main point made is the same old same old 'program with the quad should have won'. Disagreement doesn't equal controversy.
Plush wasn't the only disgruntled skater in Vancouver - Weir too claimed he was under-marked. There are complaints and criticisms of judges decisions all the time, especially during the Olympics. They don't = controversy.
And criticism has to be taken with a grain of salt when it comes from Elvis Stoijko, who has always had a serious wuz-robbed issue and always claimed that the skaters with more quads should have won. He even thought Goebel should have beat Plushenko at one worlds because he landed three quads. And he even went so far as to claim he should have been in the top three in the SP in SLC.
Ditto be wary of Bianchetti, who jumps at every possible opportunity to grind her axe about COP.
This is an opinion but not an analysis. Taking the points value of the 4/3 into account and everything else, why should he have had a 4 to 5 point lead? And who is the 'they' Plush refers to? I rather doubt it was the judges themselves. They certainly didn't need to hold back marks - didn't do so for Shen and Zhao who skated first in the Pairs SP.
Tarasova suggests the 4/3 should be worth more, and I actually agreed with that. But it wasn't at the time. Regardless of whether it was fair or not. It often wasn't fair when skaters won under 6.0 because of superior figures, but until figures were eliminated, those wins were arguably legitimate.
Here is an explanation of Lysacek versus Plush LP scores:


Here's an attempt to stir up controversy from an obscure Russian source. No links to any evidence.


This from an obscure Russian source.
Actually I was one of small group of fans who rooted for Plush over Yags. I was rooting for him in Vancouver and I just
can't stand Lysacek (to the extent that I was overjoyed that he didn't manage to compete this season). I was very disappointed with his programs. His jumps were not strong like they had been in the past and his programs were empty in terms of PCS - he clearly hadn't adjusted to the new system.
I saw the Men's LP live in Vancouver and remember thinking that if afterwards that if anything, Plush was under-marked. Although I did agree that the quad should have been worth more.
Put it this way: given how much I dislike Lysacek I was an easy target for arguments that Plush should have won. But, no argument was given that convinced me, not at the time nor since.