Very rational posting
I'll address your comparison to Street Fighter IIIs, which I've sadly only played casually, not competitively (Chun-Li's strong punch = <3 ).
There's a few things to note. First of all, when there are multiple characters with no bad matchups, the situation isn't so bad (example; Fox and Marth).
There are three key differences between Brawl and Street Fighter 3s (other than the obvious).
The first is the number of characters (39 vs 19).
The second is stage counterpicking.
The third is hitstun.
I'll address these one by one.
Number of Characters, And Their Matchup Distribution
This is the least important difference, but there are twice as many characters in Brawl, making MK's dominance even more notable as more variety should be expected.
I also want to note that, from my understanding, Yun has an even matchup with Makoto, and Chun-Li actually has a LARGER advantage on every character in the cast than Yun does, with her only disadvantage being to Yun.
Meaning, if you play any character except Yun, Chun-Li is probably a worse matchup for you than Yun is.
And finally, Makoto has no bad matchups except Chun-Li. Makoto, Yun, and Chun-Li are in the same tier because of this. Yun does not clearly dominate. Nobody suggests MK is in the same tier as the characters below him (
except Inui).
Essentially, the top three are for the most part equal, something nonexistant in Brawl. It's closer to Melee Marth/Fox/Sheik trio (Chun-Li being the Sheik).
Stage Counterpicking
Smash Bros uses stage counterpicks to increase or decrease matchup advantages. Being able to counterpick a stage beneficial to your character, or poor for your opponent, enables you to reduce a disadvantage in a matchup. Other fights do not have this.
Metaknight breaks BOTH counterpicking systems (characters and stages) by not having a bad stage, either.
Hitstun.
This is the most critical, IMO. Consider the difference hitstun makes. If you can read your opponent, even with a disadvantaged character, you only have to catch one mistake and you can punish it with a combo that takes away a significant portion of your opponent's HP, or even a super. Zero deaths exist.
In a game without significant hitstun, punishing one mistake (unless it's with a gimp, which virtually never happens to MK) is rarely enough to turn the side. You have to punish consistent mistakes. Which means that matchup gaps are MUCH MORE VISIBLE- you have to catch EVERY mistake, and when a character is capable of showing as few flaws as MK, that often means outplaying him by a wide margin.
A 6-4 disadvantage in Street Fighter < a 6-4 disadvantage in Brawl.