One common theme is power and responsibility. Since Stiles is an alpha werewolf, he has to deal with the power that comes with the title and the responsibilities of leading or protecting others. For example, in many fanfics, he has to protect Beacon Hills from supernatural threats.
Love and relationships are also common themes. Stiles' relationships with his friends, family, and potential romantic partners can be greatly affected by his new status. Some fanfics explore how his love interests react to him being an alpha, and how he balances his relationships with his new responsibilities.
One common theme is power. Since Stiles is an alpha, the story often explores how he wields his power, whether it's for good or to face his enemies. Another theme is loyalty. His friends' loyalty to him and vice versa is usually a big part of the story.
One common theme is leadership. The alpha werewolf often has to lead his pack through various difficulties like battles or dealing with other supernatural beings. Another theme is loyalty, both within the pack and towards the alpha's mate. For example, in many fanfics, pack members will risk their lives for the alpha.
One common theme is the struggle for power within the werewolf pack. The omega, being at the bottom of the hierarchy, often has to fight for recognition. Another theme is the mating bond between the alpha and omega, which can be both passionate and complicated.
The theme of protection also frequently appears. Peter, as an Alpha, may feel a strong urge to protect Stiles, the Omega. This can lead to various plotlines, from fending off other supernatural threats to dealing with the internal politics of the werewolf pack. There's often a lot of tension and drama as they both learn to rely on each other in different ways.
The theme of transformation is also prevalent. Stiles may undergo some sort of personal transformation under Peter's influence as alpha. This could be emotional, like becoming more confident, or it could be related to some sort of supernatural ability. It adds depth to the relationship between them and makes for an interesting read.
Power and responsibility is a major theme. Stiles has to learn to use his alpha power wisely while being a human. He can't rely on the natural instincts that other non - human alphas might have. Also, the theme of acceptance is there. He has to be accepted by other supernatural beings in the story as a human alpha.
One popular alpha werewolf Stiles fanfic is 'The Alpha's Mate'. It has an interesting plot where Stiles discovers his true alpha nature and finds his mate in a world full of supernatural challenges.
Love and mates are also common themes. In many alpha king werewolf stories, the alpha king is looking for his true mate. There are often obstacles in the way of this love, like rivalries or differences in social status within the werewolf community. Also, the theme of survival pops up a lot. The werewolves have to survive in a world full of other supernatural beings and their own internal power struggles.
One common theme is the struggle between the werewolf nature and the ninja way in the Naruto world. For example, a character who is part werewolf may have to balance their new instincts with their ninja training and loyalty to their village.
Romance is also very common. Alpha werewolves are usually depicted as strong and attractive, so they often have romantic relationships with other characters, whether it's a human, a werewolf from another pack, or even a different supernatural being. For example, there are many stories where an alpha werewolf falls in love with a human girl and they have to overcome the differences between their worlds.