Deviantart Description:
I know that this is a lot and huge. That's why I had taken the third gen characters out and broken the tree p into its segments, giving each of the Mane Six their own family tree. Buuut I did make a third gen and I meant to post the two big family trees (Dash, AJ, Fluttershy and Twilight, Pinkie, Rarity) too. I just kind of forgot.

Links to the smaller, easier to digest family trees, left to right:
Scootaloo & Rainbow Dash - Apple Family - Fluttershy - Diamond Tiara & Snips

I also split them up to save space in the description; each of the smaller trees contains details of those families and the links to the next gen's bio. The focus of this post are going to be the third gen characters and their families; if you're curious about any of the next gen's, just click the respective link to the smaller family tree for more info! ;)

Family of Lightning Clash/Pacific Rose:

Lightning is the son of Thunderlane and Flash Sentry. He grew up in the Crystal Empire and became a Royal Guard when he got older.
Rose is the oldest child of Big Mac and Fluttershy. She grew up on the Apple Farm, but always also liked to travel. Usually to Manehatten to visit her best friend, but as one of the new Mane Six (the element of loyalty), she traveled all over and beyond Equestria, including the Crystal Empire.
While he basically immediately had a crush on her when they first met, it was more of a slow-burn for her. She fell in love with the Crystal Empire. So after their adventures ended, she moved there to make a life of her own and after a lot of awkward pining, Lightning finally asks her out. They got together, eventually got married and have three children.
Apple Blossom is the oldest and takes a lot after grandma Fluttershy in personality, though she is a truly hard working apple at her core and eventually moves back to the Apple Farm.
Rainbow Flash is the second oldest and a huge admirer of Rainbow Dash, aiming to become a Wonderbolt himself one day.
Cloud Control is the youngest and the one to give her parents the hardest time, because she's very adventurous and energetic.

Family of Ozark Gold/Diamond Diadem:

Ozark is the son of Big Mac and Fluttershy. He's not very close to his sister, partially due to her travels with the Mane Six and partially due to her moving to the Crystal Empire later on in life. He never left the Apple Farm.
Diadem is the daughter of Snips and Diamond Tiara. She's also the leader of the Cutie Mark Crusaders of their generation, which is how her and Ozark met; both were CMC members. They started dating in their early teens and have been together ever since.
Golden Crown is their oldest, though she doesn't really take after either of her parents. She's neither a farmer nor into fashion (I headcanon for Diamond Tiara and Snips both to work for Rarity as adults), she just wants to dance.
Diamond Scepter however takes after his mother. He too becomes leader of the CMC of his generation, but he leads with the kindness of his grandma Fluttershy.

My Little Pony (c) Hasbro
My linked-in OCs and this constellation of family tree (c) Takara-Phoenix