IANAL (I am not a lawyer)
I was wondering how cool it would be to re-create a popular AAA game within a 2D isometric/indie art style.
That'd be pretty cool - this is typically jokingly called "demakes" (i.e. a 'remake' with lesser graphics).
The question: Is this all legal?
Nope, it's not legal for you to make a game that uses their intellectual property. You can make a game that uses your own intellectual property, though.
People do make 'demakes', but it's not legal. By "not legal", I don't mean it's against criminal law - you won't go to jail. But it is a violation of copyright law, which means it might get you sued. The likelihood of getting sued is low - more than likely they'll send you a "cease and desist" letter, threatening you with a lawsuit if you don't stop. But all your work would be a waste of time if they shut down your project, which is very likely.
Some studios permit things like that - Bungie let people make Halo demakes, and Valve let people make CounterStrike, Portal, and Team Fortress demakes. But most companies don't permit it - not because they are mean, but because by permitting it, it actually weakens their own legal ownership of their own copyrights and makes it harder for them to defend their property in court if another real studio tries to steal their ideas.
I know I can't directly name it after The Last of Us series
Yep, you can't name it after their game, or use any of their graphics or art designs, or use any of their character names.
and I assume Naughty Dog hasn't copyrighted any gameplay mechanics.
They can't copyright ideas directly, but if you too heavily make things similar, you might be stealing concrete implementations of those ideas, which are copyrightable.
Anyways, let me know what you think and how far I could take this cool idea.
You can make your own unique game, in your own unique game world, with your own unique characters, but have it be inspired by other games. You might even want it to be "inspired" by more than one game or TV show, mixing Left 4 Dead with The Last of Us and The Walking Dead and My Little Pony and Call of Duty's Nazi Zombies.
If you make it your own, you have creative freedom, and the intellectual property is your property, and then you can even charge for the game, or ask for donations, and it'd all be legit. And being legit is cooler than getting sued. And making money is cooler than losing money. And releasing a finished game is cooler than the game getting shut down for copyright violations.
All it takes is a little extra creativity, and you'll have your own game series.