Recently the most high quality has been the two Mario games Nintendo has made on Wii: Super Mario Galaxy and New Super Mario Bros Wii. I don't think people really give enough credit, but these games have some of the greatest attention to detail and polish that I've ever played. Whether it be graphics, gameplay mechanics, or design of levels and puzzles. It's just amazing how much polish all around there are in both of those games. You just don't see that level of quality in a lot of games... well most of them to be exact. Only that special few. There is a reason Galaxy was considered one of the best.
Now I think the Zelda series as a whole shows this high quality in a lot of areas as well. And as an entire franchise, easily the highest quality Nintendo puts out. But for most of the Nintendo franchises, there is this amazing attention to polishing the game to make it play and look as good as possible which is why i respect them as a developer so much.
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