This is a hypothetical situation. Let's say that you Naughty Dog planned on making a sequel to The Last Of Us. They asked you for ideas. What ideas would you offer? I'll post my favorites below.
[b]Story:[/b]
The plot should have nothing to do with Joel and Ellie.
The main antagonist is either Joel or Ellie, one of whom has died, and the survivor is now effectively broken beyond repair.
[b]Gameplay:[/b]
Gameplay should be more open ended, with larger, slightly less linear level design; basically you have to get from point A to point B, but you have to choose how you want to get there.
[b]Enemies:[/b]
New types of infected that have come about as the result of longer infection/mutations in the spore.
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They could have it not be a generic mish-mash of every zombie story you've ever seen before and make it an actual game for starters.