It's really hard to say. Minato is extremely fast with his Flying Raijin and is a very intelligent fighter. But Naruto has an incredible amount of chakra, his Sage Mode, and his Six Paths powers. If Naruto can get close enough to Minato, his brute strength could overpower Minato. However, Minato's speed and strategic mind might keep Naruto at bay.
In some 'minato vs naruto fanfiction', there could be a scenario where they battle in a different dimension. Minato uses his Flying Raijin to quickly move around and Naruto counters with his shadow clones and massive Rasengan attacks. Also, a scenario where they fight not as enemies but in a friendly spar to teach Naruto some secret family jutsu that only Minato knew would be really cool.
There are many out there. A really good one might focus on the emotional reactions of Team Minato. For example, Minato might be proud of Naruto's strength and how he overcomes Pain. Kakashi could be in awe at Naruto's new techniques. Their reactions can enhance the overall viewing experience in the fanfiction.
You can try looking on popular fanfiction websites like FanFiction.net or Archive of Our Own (AO3). They usually have a wide range of Naruto - related fanfictions, and you should be able to find some with the 'Team Minato Watches Naruto vs Pain' concept.
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 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.
The emotional bond would be stronger. Naruto wouldn't have to face the pain of growing up without a father. Minato could be there to cheer him on during his training and be a source of comfort when Naruto faced difficulties, like when he was bullied as a child. He could also help Naruto better control the Nine - Tails' power from the start.
Well, Minato might constantly be by Naruto's side in the fanfiction. He could prevent Naruto from taking on any dangerous missions, even if Naruto is capable. For example, he may interfere when Naruto tries to join a risky battle against a powerful enemy, saying it's too dangerous for him.
One reason could be guilt. Since Minato wasn't there for Naruto when he was growing up in the original story, in the fanfiction, he might be overcompensating for that lost time. He feels like he has to make up for all those years he wasn't around to protect his son.