Just because something is popular that doesn't mean it's not bad. There's a lot of popular media that's pretty bad.

As far as Skyward Sword goes, I'm far from the only one to think so.

There's a lot of popular media that I think is bad, but that doesn't make it bad. 

I'll bite. What does make something bad?

General opinion.

Everything that deviates from it becomes the "minority" opinion. Killing is bad, but just because most people think it is. If the general opinion was that killing isn't bad, and shouldn't be punished, we wouldn't consider it bad.

^This is the best thing to an actual answer that can be given. If it was games you thought were bad but loved anyways I could agree with you. A KNOWN bad game would be Suikoden Tierkreis (Nintendo DS), Final Fantasy XIII (PS3), ect. These games are known to be bad, but people still enjoyed them. 

Saying Skyward Sword is like me saying Final Fantasy X. There are obvious faults with the game (it's the first to have hallway maps, the voice acting is terrible, ect) but it's not a bad game. 

The fact that general consensus says something is good doesn't really mean much. It's useful, but only if you trust their judgement. This isn't the first game to have inflated review scores at the time of its release, and it probably won't be the last. 

We're getting into issues of subjectivity here, which is a quagmire in these sorts of discussion. Frankly, I'm not wrong for thinking that this game is bad unless you disagree with the basis and evidence I use to determine it. For me, it's the structure and coherency of the story and mechanics. From what I understand, you're judgement is based on what other people think. Which I think is a bit silly.

Not really a good example. Killing is bad because most people think it is, but the reason they think that way is because it is demonstrably bad on almost every basis.

Shadows of the Damned was a pretty stupid game but I had a BLAST playing it. Multi-facet pun intended.

Majora's Mask

This! And the Dreamcast port of the original Gauntlet Legends! Good times!