It boils down to technical matchups, and the problem is that, when you have two players of near-equal skill level, suddenly which character has technical advantages starts playing a role.
Let's take a basic example in matchups: Dedede vs. Donkey Kong.
Dedede as an infinite grab which works on only 5 characters, DK being one of them. Therefore, if the Dedede player doesn't screw up their timing, they can grab DK once, down throw and regrab him to 200% damage, and side throw him off the screen for a basically free KO. This is an extreme example, but an example nonetheless.
In the case of a matchup between Bowser and, say, Metaknight, Bowser is at a disadvantage because he has no real projectile attacks, all of his attacks are physical, and Metaknight has what's called a "disjointed hitbox" meaning that Metaknight's sword doesn't count as his body, so he can attack without worrying about putting his body in harm's way because he cannot be damaged by hitting his sword.
I've still slaughtered plenty of skilled Metaknight players, mind you (I've also lost to a few), but in a hypothetical situation of me facing an opponent of identical skill level, me playing as Bowser puts me at a disadvantage against my equiskilled opponent if he uses Metaknight.
Tiers aren't a new concept: they've been around since Street Fighter and they're real.
Statistically, with literally thousands of SSBB tourneys happening all the time, it's impossible to not have a relevant statistical graph of which characters are winning these tournaments. These are the proving grounds, and if no one is winning tournaments with Yoshi, it's not because no one is trying but because no one is succeeding.
You still have crazy fools like me who take Bowser into tourneys. I'm not about to change my main character because of which characters are winning tourneys, but I'm not so thick as to not acknowledge the fact that Bowser has a severe disadvantage against most other characters.
The question to ask is whether or not this has any effect on a group of people sitting around playing SSBB and that's a hard question to answer. It all boils down to how far this group of players has gone toward exploring the full potential of each character. Some characters are just the right size or fall at the right speed, etc. so that other characters can pull off some truly nasty combos on them. Case in point, the Dedede example from earlier.
It depends more upon the skill of the players than anything, but all characters do have a "ceiling" determining how far one can take them and when human potential exceeds character potential, the tier list is formed.