I'm not saying that all games that require multiple playthroughs have bad trophies, btw, just ones that don't reveal additional gameplay or story when you do. To continue the test analogy, it's like taking the same version of the same test 3 times versus three variants of the same test that ask different questions and demonstrate different facets of knowledge on the same subject. You know, like when you have a class where the teacher hands out three versions of the test to try to prevent cheating; the same basic material is being covered, but the experience is different for each version.
Tales of Xillia for example has two main characters and you choose which one you want to run through it with, which changes the narrative and reveals more about what's going on. Trophies that encourage people to experience both sides of that are good; Tales of Symphonia doesn't reveal anything extra by making you run through it 4-5 times to get all the trophies, so it's got a bad trophy list.