While normally irritated with improper punctuation and grammar when encountered in daily life, I am going to have to side with the poster above who states that Burrito Supremes is the correct way to order more than one of a Burrito Supreme. Simply put, the word "Supreme" in Burrito Supreme is not governed by the usual rules concerning adjectives in this sense. It is merely part of the entire title of that particular menu item. It would be like going to a restaurant and ordering two Salisburys steak. Obviously you would say Salisbury steaks because the entire phrase "Salisbury steak" is what you are ordering. At a normal Mexican restaurant if you are ordering two burritos, supreme style, well then yes, you would certainly say "two burritos supreme." At Taco Bell, however, a Burrito Supreme is a Burrito Supreme. Also, I am aware that there are probably many punctuation issues in this post, but frankly, everybody's human, so I don't think I'm going to lose any sleep over it.
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