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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Prequel. Joel and Tommy from the moment the prologue ends, till right before the main game begins. Keep the gameplay but expand upon it greatly. Make the game hard, very hard. Almost with a realistic take to it. Enemies should be extremely smart and unrelenting. That's all I can think of. I won't go into specifics like weapons and stuff.