As for (former) top tiers: you're forgetting Yang ;-) He was considered top tier in Arcade Edition too, and was nerfed considerably in Arcade Edition 2012 to the point many thought he was not tournament viable anymore. The game gradually went from favouring defensive characters to rush down characters, and now with Ultra Street Fighter 4, back to zoning/footsie characters: I believe Ultra Street Fighter 4 has seen the most diverse top 8 in tournaments (see Evo for example) from all iterations when it came to characters, which makes me believe that it is currently balanced quite nicely, meaning that almost all characters have a good shot at winning a tournament. Well, except for maybe Dee Jay, Honda and Dhalsim unfortunately.
For those wondering why there have been so many iterations of Street Fighter over the past few years: aside from introducing new mechanics and characters, SF has been "broken" a few times in the past with the discovery of so called un-blockable setups. These unblockable setups caused hitboxes to overlap in such a way that it would leave your opponent in a state where he/she could do nothing other than to get hit with an the attack. The only way to block it was to do it frame-perfect, which is incredibly hard to do considering the game runs at 60fps. Especially under tournament pressure :)
It was broken again with the discovery of so called vortex setups, which kept your opponent in constant 50-50 guessing state after being knocked down: will the attack hit from the front or back? It wasn't uncommon for even the aggressor to not know what side it would hit. A vortex like that could easily lead to stun, and a subsequent KO if you guessed wrong for more than 2 times. Talk about unforgiving right? ;-) Characters like Ibuki and Akuma benefitted strongly from this and almost allowed for autopilot gameplay. No fun if you were on the receiving side indeed.
In an effort to combat gamebreaking setups like unblockables and vortexes, Ultra Street Fighter 4 introduced the delayed wakeup mechanic which allowed you to mess up the timing of your opponent if they tried to do a vortex/unblockable setup. It's kind of a lazy fix, as I think it'd been better to just fix the hitboxes. Even though it does a decent job at combatting these setups, it also considerably slows down the pacing of the game as well.
As the article shows, some characters do better against other types of characters: zoning characters have historically been able to do incredibly well against grapplers for example by playing a keep-away game. Grapplers on the other hand generally tend to have the advantage against rushdown characters, and rushdown characters usually are able to blow up zoning characters. Considering that the game has been out on the market for a while, it shouldn't come as a surprise that most tournament players are able to play 2 or more characters from different "archetypes" at a high level. This "counter-picking" was historically frowned upon and considered a "cheap" move, but I believe it has become more accepted as of late due to bigger prize pots coming into play in tournaments.
I've unfortunately been able to infer how the article factored in some character specific strategies: divekicks can generally be mitigated with a fast standing jab for example, and some characters are prone to longer combo's due to larger hitboxes. It'd be interesting to see how this would affect their model as it is something that I think matters in matches: Dudley is able to do an extended bread and butter combo for example on Balrog(boxer)/Abel, which leads to not only more damage, but also more stun.
After playing the SF4 series for over 6 years, I still thoroughly enjoy playing this game in my spare time and in tournaments. I was pleasantly surprised to find out that some fellow startup founders coughTobi Lutke from Shopifycough are incredibly good at the game as well, and can't wait for them to improve the net code in Street Fighter 5. Probably has to do with being competitive I guess ;)