This was more emotional than I expected. I felt bad for Bonnie and I really like how Serena and Clemont were there for her.
...and then there was Ash, staring off into the distance. (just kidding, I know Ash cares too, but they really need to work on Ash/Bonnie)
Ash didn't have a reason to care about Bonnie. Episodes past he's had to say much harder goodbyes to his beloved Pokèmon and it's always been much more genuine than this. As I've pointed out it's not that many episodes ago that Ash released Goodra, and Goodra was with Ash much longer than Tyrunt Bonnie. That was very sad. During BW he almost says goodbye to Oshawott when he thinks Oshy wants to stay on Schalchop Island with Osharina. During the Orange Island Saga he released Laprus so it could be with it's family. In the Original series he released Butterfree, his first catch, so it can be with it's mate and start a family. And who can forget Pikachu's Goodbye, where he almost parts ways with Pikachu as he thinks it would be better for Pikachu to stay in the wild with other Pokémon - he almost has to leave his very best friend. Compared to those instances, which are much more genuine and sad, the sympathy that Bonnie is getting here is overrated and disproportionate. Even Team Rocket had to say Goodbye to Arbok and Weezing, Dustox and Cacnea (although they deserved the pain those separations caused them).
Bonnie's attitude when she learned she had to part ways with Tyrunt was spoiled, selfish and immature. Whenever Ash or another main character has had to say goodbye to a Pokémon it's always involved that character accepting that the parting is for the better and is in the best interest of their friend - It's a selfless and loving act. In Beyond the rainbow, it was Ash who suggested Goodra stay in the wetlands with it's friends, and in Pikachu's Goodbye it was Ash who tried to leave Pikachu as he felt Pikachu would be better off in the forest. In a poached ego Jessie and James tell Arbok and Weezing to go in order to protect them and in Crossing Paths Jessie released Dustox so it can be with it's mate.
By contrast in this episode Bonnie becomes bitter and unpleasant when she's told that Tyrunt has to stay in the laboratory. Everybody seems oblivious to the fact that 1) Tyrunt has a family here and wants to stay with them, 2) Tyrunt doesn't exist solely to play with Bonnie and 3) Bonnie wouldn't be able to look after him properly. It's plain selfish of her to want Tyrunt to leave it's family and travel with her simply so she won't have to feel sad at the fact that she'll never see it again. Why did she feel that anyway. Bonnie didn't know Tyrunt for that long to form such a close bond with it.
That being said it's perfectly reasonable for Ash not to "be there for her." In fact I'm surprised Serena was so comforting to her. If I were Ash I would have told her to grow up, stop being selfish and understand why this is for the best and remind her how I felt about Goodra. Ash and Goodra were together longer, and Ash didn't need a hug from Serena when those two said goodbye. If the anime has a serious recurring theme, it's that no matter how much you love someone you're always going to have to say goodbye to them eventually. And the more you love someone the more it's going to hurt. Grief is the price we pay for love.
Poor Bonnie. Forever trapped in a universe where aging up is only reserved to the monsters who evolve. She will never see that baby Tyrantrum ever again...
But don't worry. Dedenne will be with you forever and you will NEVER get another baby to take care of!
One more reason not to feel sorry for her. She had Dedenne to take care of and play with - Why did she need Tryunt. All the stuff she did with Tyrunt she could do with Dedenne. And in terms of getting another baby to take care of she does get "Squishy" AKA Zygarde core in XYZ. And she'll have to say goodbye to it too I imagine.