Okay, I'm gonna give this a go...
On a scale of one to ten for each question, I'll rate Twilight in green and Harry Potter in Purple, then give an explanation for each. The numbers I give are based on rating these two against each other. If I labeled them according to other books I liked, the numbers would be on the negative scale.
1.) Overall plot
1---2---3---4---5---6---7---8---9---10
I give Twilight a four. It's fairly cliche. Boy meets girl, girl falls in love with boy, boy screws girl, somehow it ends up happy in the end. Harry Potter gets a five because, while it has a similar overall line, there's more twists and turns and it takes a lot longer and more adventures to get there. Harry Potter is also more focused on friendship, which seems far more important.
2.) Characterization
1---2---3---4---5---6---7---8---9---10
Twilight gets a two because, quite simply, every character in the entire freaking series would fail the Mary Sue/Gary Stu litmus test. Oh my god would they fail. Harry Potter gets a six because despite the fact that Potter is also a Stu, he at least has a personality, which is far more than can be said for Bella.
3.) Keeping Canon Straight
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Vampires. Don't. Sparkle. *cough* Moving on. Harry Potter isn't exactly great with keeping with fantastical tradition, but Rowling at least tried. I'll give JKR a few points here simply because she had so many creatures I don't think anyone could keep it completely straight. But what's-her-name couldn't even keep TWO fantastical creatures to their respective traits.
4.) Reading Level
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Both seem to me to be elementary-school reading levels. Way below my ability for sure.
5.) Length
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Easy. Harry Potter has twice as many books as Twilight. To me, the longer a book or a series is, the better.
6.) Believability
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Vampires. Don't. Sparkle. Never have, never will. Though flying cars and talking paintings are just as bad.
7.) Choice of Locale
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Okay, Twilight wins this one. Washington doesn't get highlighted very often, whereas there's a ton of stories out there where the UK gets a feature. Not only that, but Harry Potter has to somehow wriggle into an alternate reality of sorts within the UK. How the heck does that work? Twilight uses real places in a rarely featured location. Could the stories fare alright if the locations were switched? Harry Potter would survive...not sure if Twilight would. So that evens the score a bit.
8.) Societal Value
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Twilight fails epically at this one. There isn't much of anything of value to be learned from it. At least Harry Potter puts a huge emphasis on the value of friendship, honesty, and responsibility.
Totals:
Twilight: 21
Harry Potter: 38
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I think Potter won this one.