If this season is going to be the last, then I think I have a perfect way to cap it all off.
The season 9 premiere starts with a force of evil coming in to Equestria. The Mane 6 managed to take it down by the end, but only just. The girls realise they aren't as connected to the elements and need to find new element barers as quickly as possible. 6 of the episodes feature the Young Six with their best qualities and by the time the finale happens, it up to the Young Six to take down Tirek and Cosy Glow once and for all. The series would close with the mane 6 passing the elements down and the young six graduating school.
I think other episodes in the season may focus on the Kirin we saw in Sounds of Silence, introducing a new student to the school, seeing Terramar interact with the Young Six (Brother/sister interactions FTW), perhaps see what Babs Seed's doing, and maybe Scootaloo's parents. That would be nice. Of course, more episodes are needed to fill the season, but