My goodness, people, I don't understand what is so complicated about this show that everyone has troubles comprehending. Everything's very, VERY simple.
There are two main characters in this show, around who evolves the main theme of the show: feeling oneself at home.
Jonathan is not a mere chicken! Learn your director already! Nishimura Junji uses chickens all the time in his shows! This is his freaking trope! Go watch True Tears if you don't believe me. It also has snow and chickens. As for Glasslip, most of the times Jonathan represents Kakeru himself. To be more precise it represents the problems that Kakeru struggles with.
Remember the 1st episode? The scene where Kakeru meets Touko at school for the first time? The dialogue about free-range Jonathan vs living in a cell? Have you all forgotten about it? If yes, it's now the best time to recall it! Kakeru, having no particular place where he feels at home, is the one who DOESN'T like the concept of free-range animals. Kakeru shows Touko how dangerous a life for Jonathan is if it's up to go around wherever it wants. Kakeru is the one who says that he'd rather live in a cell - he's tired to change his place of living all the time. He wants his home to be set in stone like a cell for an animal.
Why the heck do you think Kakeru lives in the tent? Have you ever even tried to think about it? It's so freaking simple - because he changes houses all the time, because his family always moves from one city to another! So the only CONSTANT place for him where he can sleep and feel himself home is his freaking tent! This IS his cell that always stay the same, regardless where he is located geographically.
Do you understand why there's always such an accent on the sea birds crying in the show? They DO as well represent Kakeru - they keep changing their home from season to season. They spend winter in one area and then move back to another area for summer. This is what brings Kakeru troubles and loneliness. This is what Touko felt and got scared of - Kakeru will "fly away to another place once the season changes", e.g. when it gets too cold.
So Kakeru now faces a challenge. He has two options. Option 1 - he keeps "flying" with his mum, losing Touko, experiencing the loneliness he's so tired of. Option 2 - he settles down to stay with Touko who makes him feel home here. But option 2 is also scary, because then he's losing connection to his mother and has to actually start living his own life. Kakeru is obviously scared of this heavy responsibility - once he decides to stay, he won't be able to quit if something goes wrong by moving to another place. So he's frustrated in choosing between the two options.
And believe it or not, Touko is no less scared. Having lived in this one city for so long, she's scared that her friends will leave and they will no longer meet to watch the fireworks together. Again, THIS is what the show has started with in the first episode! She wants the people dear to her to remain close and connected to each other. And what's more, she's now even more scared to lose the one who she fell in love with. Because unlike the chicken Jonathan, who can't fly despite being a bird, Kakeru can actually fly away if he decides to go with his mother.
Because of their love, because of their fears, and because of their sensitive nature, Touko and Kakeru experience and share their emotions through imagination, otherwise known as "fragments of the future". It has nothing to do with alternate worlds, fates, other dimensiona, timelines, or other bullshit - it's just their vivid imagination. They learn about each other and about each other's feelings and emotions this way. And THIS is what this show is about.
Everything that happens around them is just a romantic slice of life setting that drives this dramatic world. People meet, fall in love, some have their feelings unrequited, some have to fight for and win their love, etc. The actual drama is however between the two main characters - will they stay together or not, will Kakeru find his home with Touko or will he leave till better times, will Touko find the way to see the fireworks all together or not? These are the questions raised by the anime.
So in the end the only clear resolution that is shown is Hiro and Sachi, who are definitely shown as a couple (I'm not going to count Hiro's sister and her off-screen boyfriend). It's strongly hinted that Yuki and Yanagi are together, based on the reaction of the swim club as they run past and Hina's knowing smile--but it's not shown. As for Kakeru, the patch on the lawn where his tent used to stand suggests that he is off on tour with his mother although it is implied that he'll be back to watch the winter fireworks with Touko. I can tolerate ambiguous endings, but even for me there was just too much left hanging to be totally satisfied. It was pretty, the OST was marvelous, and if you worked really hard at it the ideas behind it were pretty engaging--but I wanted more closure damn it. (Later Edit: I didn't want to have to spend an hour going over it in my head to finally process and understand it--is probably what I meant.)
I think one of the keys to this episode were the conversations between Touko's parents, and also between Touko and her mother. We have the exchange about how her father proposed during the meteor shower, and soon after we're shown all three couples watching the meteor shower in separate locations. Touko's mother also talks about the "fragments of the future" and acknowledges that Touko is an adult (as does Kakeru's father to him in another conversation). The way her family left Touko in the care of Kakeru's also looked pretty much like a symbolic acknowledgement of their relationship ("Please take care of our daughter..." although not directly said was pretty much implied).
Back in the first episode we were given the foreshadowing that this would be the last summer that the original five friends would be together. That was true, as by the end of the summer things have changed forever--Hiro and Sachi go back to school as a couple, Yuki goes back alone as Yanagi rides the train to her modeling career, and Touko too is alone with her thoughts of Kakeru--the stranger who played a pivotal role in disrupting the comfortable world of childhood and moving them forward into adult relationships. This really was a slice of life, not in the sense we usually think of--cute girls doing cute things in a meaningless club after school--but in the sense of showing fragments of an important transition between two stages of their lives. It wasn't an easy show and it required a lot more effort than we normally have to expend to understand, but I think it was rewarding in the end.