I don’t know, I kinda like the idea. Think of it kinda like toff from The Legend of Kora. Forest hermit, stlll badass Alicorn. Or perhaps something catastrophic happened to Equestria and the only way to save it was for Twilight and her friends to sacrifice themselves.
However due to Twilight being an Alicorn, she was spared but as a result she lost all her friends and at the same time lost apart of herself, which is why she let the world think she was gone along with the others.
Just some fan theory for thought.
There may be some ways to write it that it’s done with enough tact and respect for Twilight’s character, though I’m just worried about the many ways that could go wrong. Nothing would infuriate fans of the previous show to have the main character from the previous series become evil or otherwise a hermit that just decided to stop doing things (Ala Last Jedi Luke Skywalker) for no good reason.
Twilight returning at all in some fashion is probably a big card that will be carried for a little while. Probably at the earliest the Season 1 finale (Probably more specifically, an ending stinger/cliffhangar that excites fans prior to Season 2) or if a sequel movie happens. Not just because it’s a dramatic twist to excite fans, but they’ll probably need the time to think on just how to implement it. I know it’s not a guarantee that Twilight returns, and I’m not demanding that it happens. But it should at least be acknowledged as one of the ideas they could do for a special event.
Hasbro has not declared her dead for the G5, and it was noticed that something is going on behind the scenes where powerful forces can be in the swing. What we discovered around the glass window, the three crystals that hid a spell that can only be activated by Sunny under the right circumstances and the shock of the disappearance of the Everfree forest as the fate of the harmony tree - everything points to that. Something catastrophic must have happened for the magic to disappear, and the ponies seemed to have had collective memory loss so that they do not know about each other’s fates after the collapse of magic.
Since Twilight may have been hiding and then operating in secret - it must mean that she has a powerful enemy who forced her into cover as with Palpatine and Yoda. An enemy who also operates in secret to become strong enough. It is possible that she is not alone, but also that she, like Celestia, could do little more than wait for hope. There are indications that Sunny`s fate was decided when she was born, and her father turned out to be a mysterious pony with unsolvable riddles after his passing. As we will discover in the G5. Do not think she will go out in the open, the risk that the Mane 5 will be attacked may be too great. Yoda chose to die in hope, while Luke went out with a bang - here I think Twilight will just let fate be completed and see that all her plans and hopes will bring her redemption. We may experience that she will die or ascend forever away from the world of the mortal, when her mission is completed.
Also, Twilight should be there when Sunny becomes 100% alicorn, to welcome her among the alicorns. Furthermore; it becomes more exciting when one senses that something powerful and indescribable is happening behind the scenes while the actions are taking place. It is possible that Twilight and Grogar are in a deadly game that could end with Grogar being able to invade Equus while Twilight will have anyone she needs to stop the biggest enemy the ponies have ever had. Then we will not discover them, only indirect consequences of their actions - perhaps throughout the G5 towards the final, when Sunny will face the final ordeal.
We are not done with Twilight; When she finally walks away and can join her friends forever, it will be a sad but memorable moment for all MLP fans.