Thank you for replying, sideskroll, but as it turns out though, there hasn't been a game I've played yet with perfect circles whether the Wii U Widescreen setting is on or not, which is especially made evident when GC controller button prompts appear. For some reason, the Aspect Ratio is indeed off. Also, as I said earlier, changing my TV settings doesn't fix the issue and the issue is even present on the gamepad's screen. I can link some screenshots it it helps.
That is most definitely weird... Are you launching Nintendon't from a loader, HBC or a forwarder?
Try setting "just scan" on your TV and turning OFF Wiiu Widescreen mode in both, the loader (if used) and Nintendon't.
If it bothers you that much try Devolution and enable the horizontal scaling option; it will stretch by 32 pixels and you won't notice black bars on the left or right. It's what many Wii titles do otherwise you'd see the black bars on every game.
But note that nintendont doesn't do anything to change the aspect(disregarding the widescreen option), if you compare it side by side with a GC it's the same amount of wide. Then again on the Wii U it might be different.
It most likely is because it's outputting in 1080p. So the TV is most likely just scanning what its being fed instead of applying over-scan to the image which is the usual behavior when a lower resolution is displayed on digital HD monitors.
On Wii the "advertised" resolution was 480p even though the REAL one was 448. So the TV just applied over-scan and that was that.