A group of rogue dragon slayers who have turned to the dark side could be the main antagonists. They envy Igneel's relationship with Natsu and Fairy Tail. They believe that dragons should rule over humans and plan to use their powers to subjugate the world. Igneel and Fairy Tail must stop them.
It could be one of the powerful Edolas officials who oppose Erza's presence or her mission.
Perhaps an evil dragon from Igneel's world that has a vendetta against Igneel. When it senses Igneel's connection with Naruto, it decides to target Naruto. The dragon would be extremely powerful, with abilities that Naruto has never faced before. Naruto, with his new - found knowledge from Igneel, would have to figure out how to defeat this dragon to protect both his world and Igneel's legacy.
It could be a former Fairy Tail member who turned to the gangster life. They know all the guild's secrets and weaknesses, so they can be a very formidable opponent. They might have left the guild because they felt betrayed or didn't get the recognition they thought they deserved.
It could be an ancient dragon that has been awakened from a long slumber. This dragon might have a vendetta against Ignia or the Fairy Tail guild for some past transgression.
One significance could be the emotional boost for Natsu. After so long without Igneel, having him back would be a huge source of comfort and strength. Natsu could become even more determined in battles.
One idea could be that Igneel appears in a time when Fairy Tail is facing an enemy they can't defeat. Igneel's power and wisdom help turn the tide. For example, he could teach Natsu some new and powerful dragon slaying magic that Natsu then uses to overpower the foe.
A group of rogue mages who oppose the idea of Yukino joining Fairy Tail. They might view Fairy Tail as a threat to their own plans in the magical world. They target Yukino as the 'newcomer' in the guild, thinking that if they can get rid of her, they can weaken Fairy Tail. They use various underhanded tactics like spreading false rumors about Yukino within the guild and attacking her when she is on solo missions.
It could be Natsu. He's hot - headed and might not understand Naruto's ways at first. He could see Naruto as a threat to his position in the Fairy Tail guild and start bullying him to assert his dominance.
It could be Zeref. Since he has a complex relationship with Natsu in the original story, he might manipulate things behind the scenes to make the Fairy Tail guild betray Natsu. Maybe he wants to isolate Natsu for his own evil plans.
Zeref could be a great main antagonist. His long - standing connection to dark magic and his complex relationship with the Fairy Tail characters make him a powerful and menacing figure. He could be the one orchestrating the universal war in an attempt to finally achieve his dark goals.