In the light novel, Ayanokoji is clearly the more intelligent one. He has a unique ability to analyze situations and people's motives deeply. Ryuen often falls into Ayanokoji's traps because he doesn't fully understand Ayanokoji's true nature. Ayanokoji can anticipate Ryuen's moves and counter them effectively, while Ryuen struggles to keep up with Ayanokoji's complex thinking.
I don't know for sure. The ending of such a manga can be quite unpredictable and might not have been revealed yet. You could try discussing it with other fans to get their speculations.
The development can also be based on personal growth. Horikita is often very focused on her own goals and can be a bit cold. Ayanokoji could be the one to help her see the importance of relationships. Maybe he shows her how a more empathetic approach can help in achieving their class's success. This would lead to Horikita opening up to him more, and Ayanokoji in turn would start to show more of his true self to her. Over time, a deeper relationship could form as they both grow as individuals within the context of the fanfic.
Perhaps in this fanfic, Griffith has turned into something truly evil and a threat to the world Guts cares about. Guts, being the warrior he is, might feel it's his duty to put an end to Griffith to save others. Also, Guts could be driven by his own sense of justice. If Griffith has wronged innocent people, Guts may decide that killing him is the only way to set things right.
It depends on the specific fanfic. Some fanfics might have Guts killing Griffith as a major plot point, while others could take a different direction and not have that happen at all.