This is true and that's why some tier lists are revised as far as character flaws go, but the tier list is based on how well the characters themselves pit up against each other. Plus, saying you main one character and then pulling out Meta Knight for almost all your match-ups doesn't really help either.
But, thats the difference between "main" and "only", or "main" and "secondary". For the vast majority of my fights I play luigi (you could say, I Mainly, play luigi). But some matchups just don't make sense to keep luigi out, becuase my advantage of him being my best character is negated by the terrible matchup.
Maybe what I'm saying is it seems like the tier list seems to assume you never switch characters. EX. ness and lucas being low tier. But I think that's goofy since hardly anyone plays that way. And you certainly aren't required to.
I suppose I'd feel better if the tier list reflected how good a character is to main, rather than to play exclusively. Since luigi is definetly better than low mid as a character, except some godawful matchups. That doesn't detract from my luigi game, nor many others, because I have this novel thing called a secondary.
Edit: I read back over this and it seems a bit like I'm whining about luigi's tier position. Thats not my intent here. If you'd rather, please switch out luigi for ness, lucas, bowser, or any character who's held back on the tier list because of specific bad matchups.