Many if not most Naughty Dog games have too few checkpoints. There are parts of games like the Uncharted series where difficult sequences can take 15+ minutes and it doesn't save until after you complete the entire area. A lack of saves is one thing that has always grinded my gears about Naughty Dog games.
I'm way more upset by how little they are moderating online games for The Last of Us. There is some blatant cheating going on in that game. They need to ban users and release a patch for MP to fix some of the glitches/exploits.