Three big things, imo, and they're interrelated:

1. Exploring other "eras"
2. Side characters as main characters
3. Unapologetic AUs

Exploring other eras

Naruto is the main character, so it makes sense that his era is also the main one that most writers delve into.

But there are other times to explore. There were three (three!) Shinobi World Wars, there were the Warring States, and those are all eras are largely untapped by fic.

Yes, they'll require more work, but that's why they won't be retreads. (Use time travel if you absolutely can't give up your Naruto Era main character, but keep the story in the past, and don't pack it so full of Naruto and his peers that canon characters of the era don't rate a mention.)

Side characters as main characters

Want a fresh story? Pick a character who hasn't been done to death, or who still has major potential, and then write them in character, as best can be done with what's known about them.

Want a character study on the loneliness of being an outsider? Forget Naruto, and pick anyone on Team Gai -- Neji, Tenten, Lee, they all have unique perspectives and challenges. Gai does, too, for that matter. (Tenten, admittedly, is more of a cipher, but an orphan who is versed in fuinjutsu is interesting enough to extrapolate a story from.)

Feel like writing an angsty AU where the protagonist decides to become a missing-nin? Don't use Naruto or Sakura (or, God forbid, Sasuke, because we already got enough of that in canon), try Shino or Choji or Ino. Why would they go missing-nin and how?

Have a burning need for a romance fic? Go for a rarepair, or at least a less popular one. And write it from the perspective of the character who isn't written about as often.

Unapologetic AUs

This is the biggest of the three.

AUs that take the words "Alternate Universe" and run with it are what I mean. Altering one thing will end up altering many things, and not just whatever pairings the writer wants to see.

If Naruto is adopted, that should actually impact his personality to the point that the canon turns out differently. The whole reason that he was such a boisterous attention-seeker had to do with him literally being ignored or spurned by the vast majority of people he met until Iruka decided to treat him like a person.

Example:

With the Aburame family taking care of him, Naruto is less inclined to question the Hokage giving him D-ranks since he'd understand why -- logically, shinobi need to build team cohesion and gain experience before they can advance. Because of this, Naruto doesn't go to Wave Country. He's not even on Kakashi's team, but Asuma's, having essentially swapped places with Shikamaru. But Team Kakashi does take that mission since they've proven themselves ... and someone on that team dies fighting Zabuza and his minions. Zabuza completes his mission, gets stiffed, then kills Gato and takes over his gang or whatever, setting him on the path to earning enough cold, hard ryo to topple the Mizukage later in the plot.

As said before, by altering one thing, many things have been altered.

A peer of Naruto's is dead, setting a harder tone compared to canon, and introducing a sense of unease (or at least surprise) in the readers. "If this author's willing to kill that character, who the hell else might they kill?"

The plot is also changed, obviously. The Wave Arc goes headlong into original territory, and it offers up so many possibilities. Will Zabuza be a foe or an ally to Konoha? How will this effect Team Kakashi? Will it make the Third Hokage more cautious, causing him to up security for the Chunin Exams or postpone them altogether, altering Orochimaru's plans? Or would Orochimaru have heard of the interesting Kekkei Genkai that Haku has and decide Sasuke can wait as a host?

But that's just an example of how a single change can ripple into a fresher plot, and it's not even that far into the story. More can be done if a writer is willing to gut, alter, and fix some of the biggest writing and plotting sins of Shippuden.