You keep repeating the 2quads/2 3Axels, but at the end Hanyu had +5 points in BV over Machida in the LP. Were those points undeserved? Those 5 points are the main reason he managed to scrap the win at all, since his LP PCS weren't even a point higher than Machidas (who btw also had some pretty tight landings).
In comparison, in 2012 Daisuke actually had a higher BV than PChan overall, and lost the title because of PCS. Now if you couple that with the fact PChan had more visible mistakes than Daisuke I think it's quite obvious why for most people 2012 is more questionable than 2014 (plus the winning margin of Chan being way higher than Hanyus lucky 0.03).
Higher BV yes (you forget that Chan had 2.1 higher BV in the SP, though), but Chan had higher GOE (particularly on his quad jumping passes) which made up for that... with 5 points higher BV, and with Chan falling, Dai and Chan still ended up with similar TES scores. Other than his first 3A, Dai didn't have more than +1.00 GOE added to any of his jumping passes -- Daisuke's total GOE on jumps was just +2.74 points. Chan's total GOE on jumps was +7.99 points. Dai's 4T got 0.14 GOE, Chan's/Hanyu's got 2.43.
If we're talking SP, Chan had BV of 41.4 and Dai had 39.3 (a difference of 2.1). But Chan again with higher GOE got 2.81 higher TES scores. Dai's score was particularly compromised by the -3's of the 3T<< being applied to his 4T (which I don't agree with but that's the points system). If he had left that nice quad alone, that would have got him about 11-11.5 points for the opening pass instead of 8.74, and then adding the 3T to the 3Z later on with no error (which I'm sure he practiced in case he missed the quad) would have gotten him about 10.7 points instead of 7.3. Right there he could have made up about 6 points. And of course, there's the 3F< in the FS which lost him about 3.4 points. So, while of course, the judges hosed Takahashi for PCS, Takahashi didn't have the GOE of Chan, didn't have the extra quad of Chan, and made errors that are costly in terms of points under IJS.
Visible mistakes in the FS, yeah, Chan had one (maybe 2 if you consider the minor foot down at the end of the series). But "visible mistakes" aren't what counts under IJS - otherwise many would say Dai did a "perfect" Worlds 2012 SP because to the audience he didn't make any obvious error on the 4-3 (this was unfortunately a tendency with Dai's jumps as they regressed in the later years of his career - he would skate clean but get downgrades/URs, so visibly "clean" programs actually lost him lots of points technically). As I said though, errors like URs/<< weren't as severe under 6.0 so Daisuke definitely would have won 2012 Worlds if under 6.0 but the IJS rules are detrimental to him because they not only catch his rotation errors, they also give more grade of execution to Chan (whereas under 6.0 it probably wouldn't have made much difference, Chan's jumps being better quality than Daisuke's, as long as Dai went clean or looked like he went clean).
We've seen it with other skaters like Kanako or Mirai - give a seemingly clean skate but then get nailed with URs, and the audience might boo because they think the skater went clean, but technically speaking the skater made many errors which would be reflected by the points.