Sonic-Dude that over thought out article almost reminds me of those endless bloody arguements religons have over which is the right version, I'm not going to be technical over something that tries to be deep but isn't, but here's the 2 cents of an old skool sonic fan.
For starters the meanings of the plot changes are just SEGA, fleetway or whatever company involved trying to make the sonic universe more appealing to their target audience. Apart from maybe the comic they have mostly failed at it, but hey we now have about 8 different versions of the sonic universe so full of plot holes it's impossible to link them all together.
Cliche as it may sound but I tend to compare sonic games with how mario has done now. Most of the time his game plots and vocabulary remind me of something out of a carefree pre school cartoon, but at least they get the gameplay right. Sonic tries to take the opposite approach for the most part and they can't even get sonic's image, storyline or universe right.
edit:
Dear god don't even get me started on the sonic fanbase, it's probably half the problem. I think it has to have one of the highest ratios of varied fans in all fandoms, from normal gamers to deluded freaks.
Jam it back in, in the dark.