Yes. It's easier to win against everyone as the top characters of the game, and harder as the NOT top characters of the game. Your friend might have won against all of those, but it's only because his characters have the tools to give him wins easier. You, on the other hand, outskilled him and his usage of those tools, but when faced against other players, you get outplayed by THEIR tools/skills.
In conclusion, you outskilled him. I feel the same way whenever my Snake-maining friend beats me and everyone's like "Oh, Kewk, you lost against him! He's better!"... When they don't even realize half the time it's that Snake/MK have better tools than Kirby, and it's not entirely because he's more skilled than me... >_>
Not saying I'm more skilled than him, but that wins/losses aren't attributed just to skill, but to your characters' traits as well... And I don't always lose, literally it's been 60% of his wins lately, but at other times it's the other way around.
EDIT: What I said also explains why the most notable top players are people who main MK and Snake... M2K, Ally, Dojo, Tyrant, etc etc... They ARE good, but probably comparing their raw skill to other top players, they could either be even, slightly worse or slightly better. Yet they get more recognition and win more matches thanks to the tools they've decided on using.