“9” came out on 9/9/2009 (heh), and was somewhat overlooked because the director, Shane Acker, was a no-name nerd, and although Tim Burton was a producer, his name wasn’t prominent enough in the pre-prod. The film does come off as Burton-esque, and part of its unappeal to some audiences was that it couldn’t decide if it was for kids or adults. It’s got animated dolls (Stitchpunks) and action, but it is about the end of humanity, and a lot of the action is violent, and the way the dolls get their lifeforce sucked out is the stuff of nightmares.
1. The protagonist characters that die, stay dead. Their bodies remain intact, mostly, but most writers would have the living Stitchpunks try to find a way to reinsert the lifeforce back into the bodies, which would be the Scientist’s actual solution. Instead, they are dead for good, though their souls are still intact, per the Scientist’s design.
2. 1 isn’t killed by the rest of the Stitchpunks but “redeems” himself. 1 comes off at the antagonist in the group, but he sacrifices himself for 9 in accordance with his life philosophy. I put “redeems” in quotes because he didn’t require redemption since he’s actually the main protagonist in 9. We’re groomed to think 9 is the good guy because we’re introduced to him first and he has a generally likable innocent personality, while 1 is has those narrow, unforgiving eyes and dresses like a Catholic Bishop. Based on this alone, who would you root for? Yet, 9 starts off by getting 2 killed, then arrives at the sanctuary and continues putting everyone in destructive situations—something even 9 himself admits. 1 is trying to keep everyone alive and safe, and now he has to put up with an over-curious interloper who puts everyone in danger. Wouldn’t you be something of a dick like 1 is?
3. 9 should have stayed a mute. When 9 wakes up in the Scientist’s apartment, his voice box mechanism isn’t set correctly, which was fixed soon by 2. Having him designed to be silent would’ve been a part of a great plot element, where all of the Stitchpunks hold a different part of the Scientist’s (therefore, future humanity’s) soul. They already are very different, personality- and ability-wise, so the effort to massage that into the story be so hard.