This is a very interesting thread.
First I'd like to highlight the amazing work of the authors of the story of the game, especially the character design part. Here we are playing a fan-made pokemon game, yet discussing the relative sadness of childhood tragedies.
Secondly, I would like to bring some attention on two cases who, in my opinion, are at least as sad as Taka & Charlotte (who I agree are very solid candidates for the saddest character of the story) : Luna, and Terra.
Luna is the daughter of Elias, which is in itself a strong cause of sadness, given the mental state of the man. She was raised in the same purpose as Taka, as he tells us in the Desert, and if El may not have been as rough as Solaris, I doubt he gave Luna much love. In fact, Luna's personnality and choice of life (constantly running away from anything or anyone that could threaten her freedom) are good ways to understand how sad she is.
Besides being the Dark-type Gym Leader (I mean, not very subtle), she likes to live in the dark, alone, she likes fairy tales and fictions (she's often role-playing and her Pokemon are named after "Alice in wonderland" characters or creatures), and she likes dramatic speeches with ancient and literary vocabulary.
And
To conclude, Luna is a very charismatic yet dark character, who seem to wander through the game without any strings or purpose, seeking nothing but peace.
Regarding Terra, it's simpler. She developped a completely crazy personnality (even breaking the 4th wall and laws of physics) to cover up her sadness. She has no friends, no goal. Her parents, though alive, are passive people just witnessing the life of their daughter without seeming to really care. The only person that mattered to her is Lin, who potentially manipulated Terra into joining Team Meteor.
And she had an awful end if you ask me. Getting locked into a virtual world doesnt seem very fun.