In a God Eater 3 and God Eater 1 fanfiction, the story could center around the sharing of combat techniques. The more experienced God Eater 1 characters could teach the God Eater 3 characters some of their old - school but effective ways of fighting Aragami. At the same time, the God Eater 3 characters could introduce the God Eater 1 crew to the latest weapons and upgrades, leading to a more united front against the Aragami menace.
There could be a story where a God Eater from God Eater 1 is brought to the future in God Eater 3. They would be out of place at first, but then start to adapt. They might see how much the world has changed in terms of the way people live, the technology used in fighting Aragami, etc. This could lead to a great character - development story as they learn to fit in and contribute to the fight in the God Eater 3 world.
Sadly, Soul Eater didn't cover the entire manga. The anime made some cuts and changes to the story, leaving out certain plotlines and characters that were present in the manga. This was probably due to various production and time constraints.
No. The Soul Eater anime didn't cover the entire story. There were some plotlines and character developments that were left out compared to the original manga.