what you are calling wrong aspect ratio is actualy the correct one, nintendont jsut outputs the native stuff the game gives and then the gc itself would fit to perfect 4:3 or 16:9 so yeah the tiny issues your missiong screen left and right is becuase the game didnt output that far and the gc just stretched it to fit 100%.I tested only two games. Metroid Prime and Evolution Worlds. Metroid Prime have broken aspect ratio too. Broken in another way.
Also, i downloaded Dolphin and made comparisson. Now i'm confused. Dolphin reproduce exactly the same aspect ratio but proportions didn't broken. I played around with nintendont settings and find that with "Force PAL480p" proportions look right and almost identical to Dolphin: http://screenshotcomparison.com/comparison/209542 Nintendont just slightly cut off image. But i can live with that.
wiiu widescreen is just to fill the screen instead of 4:3 but try to mess with the width setting and choose a value to your liking, but be aware that manny games crash with width hack so its only recomended if you cant live without that tiny inch of the screen.