First image that immediately comes to mind is the bare tree. The tree is dull in color with minimal leaves; either the tree's health has been deteriorating or the tree is already dead. Want to know what else was dying in the first half of the episode? Stoutland. That Pokemon tended to sleep underneath a bridge right next to that tree. With all this in mind, you can say that tree symbolizes Stoutland and the condition it's in.
Now, note that in various moments in the first-half of the episode, one leaf gets blown away from the tree. With each leaf carried away, we see Stoutland's condition worsen. The final leaf from the tree is blown away the moment Stoutland dies. Thus,
the tree signifies a countdown clock to death, with each passing leaf indicating a deteoriation in the Pokemon's health. When all the leaves are gone, the tree has lost all life. Likewise, Stoutland's condition deteoriates over the course of the episode to the point of death.
And once Stoutland dies, we see Litten grieving over Stoutland's death. For the duration of it, the episode changes to a gray-coloring instead of the usual, cheerfully bright colors. This highlights a tone change, one that not only affects Litten but even those surrounding it. Ash and Kukui become quite sorrowful watching Litten cry, and we see how gloomy Ash looks when thinking about the Pokemon. This gray-colored tone continues even when Ash buys food and brings it to Litten, which shows that no matter what kind act Ash does for it, Litten continues to grieve.
It's also worth noting that rain pours the moment Litten realizes Stoutland died. Due to its chaotic nature and similar properties to tears, rain commonly symbolizes grief and turmoil. The rain ultimately symbolizes Litten's grief.
The symbolism only gets more interesting with this clip:
As you can see in these two screenshots, Ash and Kukui are watching Litten grieve from a distance. A dark shadow separates the two individuals from the Pokemon. On the other side of the shadow, Litten is all alone. The shadow ultimately conveys Litten's deep feelings of loneliness,
especially when its father-figure and the only family it had passed away.
Now, going back to Stoutland, the final leaf blows from the tree and onto the sofa that Stoutland slept on. When it rests there, Litten stays on that bed for the time the leaf is there. Like we previously examined, the tree symbolized Stoutland and its deteoriating health, and it ultimately served as a countdown with each passing leaf. The final leaf marks Stoutland's death, but unlike the other leaves, it doesn't just fly away. It lands on a location close to Litten instead... on a location that was dear to the Pokemon. To me, this must've been Stoutland's way of accompanying Litten without being physical present in this difficult time. It's like it's physical presence just faded away, but it's spirit hasn't passed into the afterlife just yet...
...which leads me to the next symbolism. There came a point where the final leaf blew away from the sofa, but at that moment, the rain stopped and the colors returned from gray monotones to bright colors again. When Litten wakes up, it sees a cloud formation of Stoutland, complete with a rainbow in front of it. Rainbows signify happiness, and when they follow after death, it usually means the deceased individual has finally found peace. You can apply this to Stoutland. When it died, it probably didn't achieve peace right away, as evident by the gray monotones and the leaf's presence of the sofa that Litten stayed with. Now, with the cheerful colors and rainbow in the sky, it seems that Stoutland has finally passed into the afterlife. The cloud also seems to nod to Litten, and Litten no longer grieves. From that, the color tone change and the cloud's movement represent the moment Litten has learned to move on.
In all, what makes this episode so brilliant is that the symbols and the color tones highlight Stoutland's death and portray the various feelings Litten experiences in response to it.
On some other minor notes, I really liked how Meowth factored into this episode. You can tell that it developed a bond with the Litten after that scuffle in the episode where the starter trio was separated from their trainers, and Meowth seemed to pick up on the tragic events. Probably my favorite Meowth moment was when the Pokemon was looking up at the ceiling from within Team Rocket's base. As Meowth worries about the situation, Bewear comes up and hugs Meowth. Normally, Bewear intervenes in a comedic scene where it hugs Team Rocket and takes them away, but here, we see a much more caring side to Bewear. The contrast from the humorous hug to one of emotional warmth adds to the nature of what is going on.
There is no doubt Stoutland's death will go down as one of the most emotional scenes in the anime in recent years alongside Clembot's death, Bonnie singing that sweet song to free Puni-chan from Team Flare's control, the final DP episode, and a few others I can't remember off the top of my head.