It's one of the reasons I really dislike this game. The whole game is about counter picking, so you can never really tell who is the better player and unless you pick a generic all-rounder like Ryu, Akuma or Guile (and now Chun?) there will be be some seriously biased matchups.
Though i agree that counter picking makes it easier to beat a certain character, i do feel that with enough match practice you'll be able to overcome hard matchups.
If we look at Guile for example, with the amount of time i've played against him, i know exactly what i can and can't do, so if you play it cleverly, you should be able to overcome it, as Balrog has the tools to win.
There are some horrible matchups like Sagat v Zangief, and Dhalsim v Deejay, where it's almost impossible for the latter to win, but most machups are around 5-5 or 6-4, and enough match practice will prepare you.
It also depends on what you consider makes a better player.
Does someone with great exeution make them the better player, or someone with great fundamentals?
I tend to think that someone who has the better fundamentals to be better, a player with great execution can be flash all they want, but if they don't have the basics down, they're gonna get beat everytime by solid footsies.