All the locations are symbolic.
The game starts with the last remnant of the US Government in Boston, which is appropriate because Boston was a starting point for The American Revolution so is arguably where the country began. The last act is in Salt Lake City, a city that was founded by survivors amongst other subjective terms for The Mormons. Someone explained the symbolism of the Colorado University on YMMV page under Genius Bonus. Lastly I posit that the reason for Jackson, Wyoming is a reference to the song "Jackson", a song about a couple in a dead relationship coming to Jackson for a better life than being with their partner. The reference casts further doubt over the sustainability of Joel and Ellie's relationship. The last cutscene is even called Jackson. You've got me on Pittsburg though."Find something to fight for": parents letting their kids down
Joel lets Ellie down massively when it comes to the cure. But here's a minor example at the end - when Ellie talks about Riley and Tess and Sam - he assumes she's making a cry for help. An emotional cry for help. But she looks disappointed when he touches his watch and talks about finding something to fight for, and given the Word of God on how she saw through his bullshit, this is perhaps one more thing she saw through - Joel was trying to convince himself that he had made the right choice. And she realised that then, on top of his talking about Sarah on the way there.
At the same time, she's also disappointed because of this: she was talking about what she was fighting for. Ellie pushed on through a year of hell to the hospital. She could've given up along the way. She could've given up so many times. But she didn't. She was fighting to save people - to save the crashing plane of humanity. She saw the journey as a chance to help people. And he didn't understand that, because he was busy focusing on the justifications of his actions (again, his insistence on recalling Sarah, and his touching of his watch. She's clearly on his mind). Also, it's odd advice to be giving someone who had to fight on her own - she had to fight for Joel in Winter. She fought for him. This ties into his not accepting that she's grown up - that she has changed, that she's a very different little girl from what Sarah was or would have grown up to be.
Of course, it's also ironic - he just stole what she was fighting so hard for from her. He didn't give her the choice to take the pilot's seat, and let the plane go down. He robbed her of the thing she was fighting for.
Joel is unable to see through to the heart of it all - that Ellie is mature. That she's gone through the crucible of hell and come out independent and brave, and that she can make choices and has her own goals to fight for. It's an additional layer to the idea of him depriving her of a choice to save everyone, and also adds to the fact that the writer tried basing Ellie off his daughter. This is an acknowledgement of the fact that parents can fail at recognising that their children 'are also people with agency and choices and dreams of their own.'
