I don't see what difference it makes that the less popular team wins. It is because that team wins the most matches. That means they performed better overall than the other team. How does being less popular negate that? Literally has nothing to do with popularity.
However, the less popular team is STILL playing better and winning more. Your skill isn't affected by the team you picked. You don't "not earn/deserve" the win because you picked a less popular team.
You are basically undermining the fact the winning team just had better players, solely because it wasn't as popular.
Just because you are good at Splatoon doesn't mean you are going to like the most popular option.
There is actually a science to how some of this works too. Sometimes, the underdog in games wants their win more and tries harder, while the likely winner is more cocky and performs worse.
We don't know, but no. The problem is not the popularity.