One of the main similarities is their self - sacrifice. Minato sacrificed himself to save the village and his son. Naruto has also shown that he is willing to put himself in harm's way for the greater good. He's always the first to jump into a dangerous situation if it means protecting those he loves. Another aspect is their leadership qualities. Minato was a great leader as Hokage, and Naruto has developed into a great leader as well, inspiring those around him.
Kushina could be an important character even though she's dead in the original story. In this fanfic, her spirit or memories could play a role in Naruto's upbringing. For example, Minato could tell Naruto stories about Kushina's feisty personality and her love for the village.
In some fanfictions, Minato saves Naruto physically. For example, he might use his teleportation jutsu to appear right in the middle of a fight and whisk Naruto away from danger. In others, he could save Naruto spiritually. He might enter Naruto's mind, like in the fanfic 'Minato's Mind - Saving Mission', and give him the strength and confidence to overcome his inner demons. Sometimes, Minato saves Naruto from a political situation. For instance, in 'Minato and the Hidden Leaf's Politics', he uses his influence and wisdom to protect Naruto from being used as a political pawn.
Minato would likely be extremely shocked. Naruto is his son, and the idea of Naruto attacking him would be completely unexpected. He would probably try to talk to Naruto first, to find out what is wrong and why he is being attacked.
One common ability is their speed. Minato was known as the Yellow Flash for his incredible speed. Naruto, with his Sage Mode and later forms, can also move extremely fast. Another is their use of the Rasengan. Minato created the Rasengan, and Naruto has mastered it and even developed it further.
One possible reason could be for Naruto's protection. Maybe Minato knew of some great danger that was coming for Naruto and he thought that banishing him would keep him out of harm's way. Another reason might be related to some prophecy or hidden power within Naruto that Minato feared could be misused if Naruto stayed in the village.
Sakura could be another main character. She might be shocked by Naruto's arrest and start her own investigation. Maybe she teams up with Sasuke, who also has his own complex feelings towards Naruto. Their combined efforts could play an important role in uncovering the truth.
One popular theme is Minato getting to know Naruto in the afterlife. Since Minato died when Naruto was a baby, fanfictions often explore their relationship in a spiritual realm.
In the 'naruto is more like minato fanfiction', their relationship with the Nine - Tailed Fox could be similar. Minato sealed the Nine - Tails within Naruto. So, in fanfiction, Naruto might show a deeper connection to the Nine - Tails that is reminiscent of Minato's understanding and handling of the powerful beast. Maybe Naruto has an easier time controlling the Nine - Tails' power because he is more like Minato, as per the fanfiction. This could also tie into their overall power levels, as both being strong shinobi with a special relationship to the Nine - Tails.
In fanfiction, Naruto and Minato often represent a connection between generations. Minato was a great ninja in his time, and Naruto is following in his footsteps. Fanfictions can explore how Naruto lives up to his father's reputation.