Okay, it might be just me, but . . . those five jewels look like they're somehow representing the Elements of Harmony, or at least the rest of the Mane Six . . . Odang. Now it looks like the Mane Siz are actually somehow imprisoned inside the crystals or something . . . I might be over-analysing, but if I am, the similarity to what my mind is telling me is uncanny.
A year has passed. But she felt like it was yesterday.
Coming to the tower she passed by her myriad crowd of servants and soldiers. Each of them regarding Dark Queen Twilight with fear and grudge. But all averted her glare as she gallops on. But here, her true self emerged. She lay at the centre, in the midst of the five crystals, each holds the spirit of her friends. Friends that she sacrificed for forbidden power, amongst countless others.
Her broken circlet remained undisturbed on the ground. She remembered her former teacher's last words. "Was it worth all this?"
Her answer in the past was in contrast with her answer now. She broke into silent bitter tears, repeating the same words for the past hundred moons...
One thing to remember is that the elements of harmony are the last resort weapon. Nightmare Moon and Discord were deities capable of great harm to the whole world. Chrysalis had an entire army that threatened to bring all of Equestria to ruin. Sombra was one unicorn solely focused on the Crystal Empire. His threat to things over all paled in comparison to any other threat presented to us in the show thus far. Sombra wasn't enough of a threat to justify using them or risk losing them in a far away land. Just something to think about.
Actually, he was a threat to the world. Remember toward the beginning of the episode? Celestia said that if the empire is filled with hope and love, then it's reflected across Equestria... and then she very, very heavily implied that hatred and fear would do likewise.
Consider that Celestia is a deity for a moment. Deities always have plans. It isn't enough just to reharmonize or turn Sombra to stone. Celestia needed Twilight to learn about self sacrifice and for Cadance to be in a position where the crystal ponies would undoubtedly view her as their leader, as she had just proven her love in the battle against Chrysalis, therefore being the prime candidate for a role where love powers the kingdom.
Now, Celestia has become further ahead in her plans with Twilight, and set in stone a proper ruler for the Crystal Empire.
Deities always have plans, for all we know, Celestia could have purposely lost to Chrysalis just so that Cadance and Shining Armor would be forced to prove their love in the off chance that the Crystal Empire does show up.
If they used the Elements of Harmony then Twilight might have never found the crystal heart, since she wouldn't have had need to, which means that she would have never learned self sacrifice, and Cadance would likely have never been seen as the ruler of the Crystal Empire.
More importantly is about Twilight though, as the episode was almost solely about her.
All good and well said, but... I'm not trying to make the point that the elements should have been used. I'm just saying that the argument of, "They weren't needed because Sombra was not a significant threat," isn't a good one. Your argument is much better, even if based on the assumption that Celestia is a diety. Of course, it doesn't address the original concern that the elements are losing their purpose in the series in general. For that, MidnightWonko down there makes the best argument.