Maybe an enemy spy who has infiltrated the little soldier's unit. This spy would be constantly trying to undermine the unit's operations and would be a constant threat to the little soldier and his comrades. He could be very sneaky and hard to detect, which would make him a formidable antagonist.
An arms dealer could serve as the main antagonist. He supplies weapons to both sides of the conflict and doesn't care about the lives lost. The little soldier might find out about his unethical practices and try to stop him, but the arms dealer would use all his resources and connections to keep his business going and get rid of the little soldier.
It could be a power - hungry leader from one of the main factions. For example, a strict Erudite leader who sees the little soldier as a threat to their plans of total control over the society through knowledge and technology.
Perhaps an evil organization similar to the Akatsuki. They hear about the unique abilities of the little boy and decide that he would be a valuable asset to their plans. Their leader could be a mysterious figure with a vendetta against the Hidden Leaf Village and sees the boy as a way to get revenge.
It could be that there is a mastermind behind the creation of the chaos soldier. Maybe a rogue ninja who wants to use the chaos soldier to overthrow the existing ninja villages and take over. This person would be pulling the strings and be the true antagonist while the chaos soldier is more of a tool.
A powerful dark dragon could be the main antagonist. This dragon might be jealous of the little flame dragon's unique abilities or position within the dragon community. It could constantly try to undermine the little flame dragon and cause trouble for it.
It could be a human fisherman who has discovered a way to capture mermaids and is hunting them down for their valuable scales and tails. Aquata has to stop him before he wipes out all the mermaids in the area. Or perhaps an ancient sea monster that has been awakened from a long slumber and is causing chaos in the ocean, and Aquata is the only one brave enough to face it. This sea monster could be very difficult to defeat as it has powers that are unknown to the mermaids.
A sea witch could be a great antagonist. She might be jealous of Attina's beauty and grace, and try to use her magic to turn Attina into an ordinary fish. The sea witch could also create all sorts of obstacles for Attina and her friends, like summoning sea monsters or causing storms.
A powerful sea witch who is jealous of Marina's beauty and popularity among the mermaids could be the main antagonist. She might try to steal Marina's voice or tail to make her powerless.
It could be an old, grumpy neighbor who is constantly annoyed by the eight little hellions' antics. He tries to get them in trouble at every turn and devises all sorts of plans to make their lives miserable.
It could also be a new villain who has somehow managed to hack into the Winter Soldier's programming and redirect his mission towards kidnapping Tony. This villain might be someone who wants to create chaos between the Avengers by pitting the Winter Soldier against Tony. They stay in the shadows, pulling the strings while the Winter Soldier and Tony are caught in the middle.
In a more unique take, it could be an entity created by the combination of modern - day technology and dark chakra. This entity could sense Naruto's powerful chakra in your house and see him as a threat to its plans of taking over both the Naruto world and our world, so it tries to eliminate him.