4. Yes, There Are Arbitrary, Plot-Convenient Powers...
Could have saved us a whole lot of time by just predicting the ending upfront.
One of the most aggravating aspects of the Twilight saga - aside from it calling itself a saga, which is an insult to any classical works bearing that term - was the way each vampire had a completely different special power, so that by the end of Breaking Dawn it felt like the lamest X-Men spin-off ever.
The Mortal Instruments explains away many of its powers with the aforementioned runes, but then suddenly gives Clary the power to turn 3D objects into flat paper drawings. Why? Well, it sure does help the plot along, but at least in this movie, it's never explained. And since it only seems to work on animate objects, it's not a helpful gift in most normal situations - turning enemies to paper dolls would be cool, but either she never thinks of that or she just can't do it.
4a. ...They Need Them to Fight Bats and Lava-Monsters.
Your movie can't suck too badly if you have lava monsters. It is funny how they never think to use the animate water in the portal to snuff out the beasties' flaming embers, but there's probably some canonical reason for that which won't be explained until the fifth film that may or may not ever be completed.
The silver snake bracelets that turn into whips are cool too.
5. It Doesn't Seem to Make a Lot of Sense Overall.
Again, the books may explain all things perfectly, but those of us not inclined to read them just have the one movie to go by, and we wonder things like why the secret world of all these supernatural creatures seems so sparsely inhabited, why those guys at the graveyard have their mouths sewn shut (besides looking cool, circa 1995), and how arch-villain Valentine's plan appears to hinge on the fact that we don't already realize a "W" looks like an upside-down "M," or that plunging a bunch of swords into the ground in a Pentagram shape isn't all that effective if even one can just be pulled out again.
And how is it that Clary's mom was so hard for the evil forces to find when one was living in her building the whole time? Is this a magic world with no Internet or phone books?
5a. ...But at Least It Has a Sense of Humor About That.
Seriously. Twilight's version of humor was to have the characters go see a movie called Face Punch. The Mortal Instruments busts out a gay warlock named Magnus Bane who walks around parties in his tighty whities. Advantage: TMI (the book-title acronym, and the too much information). Also, the characters here make pop-culture references you've heard of, from Close Encounters to Ghostbusters. They even rope in Johann Sebastian Bach and name him one of the original Shadowhunters.
On the other hand, I think the benevolent angel Raziel is proof that Clare does not play video games.