Yes, he's still probably in love with Mikasa. As the original asker stated, it's been a long time since Jean acknowledged Mikasa's feelings for Eren and his inability to stop them. But the fact that his love isn't reciprocal, if it's genuine, doesn't stop it from being. Valuable.
Because your question states "most likely," the answer is no. Mikasa is not the "most likely" to marry Jean. She is most likely to end up with Eren because she is madly in love with him! And I believe Eren likes her as well but is unaware of his sentiments.
Yes, Eren adores Mikasa, who is the second most important lady in his life after his mother. Despite this, Eren and Historia may marry—more out of duty and responsibility than love.
Mikasa is a famous warrior who fights alongside Eren as one of the 104 Divine Generals. She is also the first person to discover his ability to transform into a Titan. When she sees this strange transformation taking place before her eyes, she instinctively knows that it is something special and that Eren should be allowed to grow up with hope instead of fear. Thus, she accepts him even though he is very aggressive when they first meet.
When Eren returns home after five years in captivity, he finds out that Mikasa has married his friend Bertolt. However, he still loves her and they can never really escape their past feelings for each other. Even so, she decides to stay married to Bertolt in order to protect him and Eren from the horrors that live in the outside world.
However, when Eren becomes the target of attack by another giant creature called a Paradiser, he realizes that there is no one else who can stop these monsters except himself. So, he transforms into a Titan again to fight for his life...
Eren, The program shows Eren and Mikasa's emotional connection as flirty, and it implies multiple times that Mikasa is committed to Eren in a way that isn't dependent on being his brother. Several other characters refer to Eren as Mikasa's lover, and though she resists, she generally blushes when she hears this. They seem to get along well and have fun together.
Also, Eren seems to respect her opinion and wants to learn from her. He often asks for her advice on matters of strategy or life.
In the final episode of the first season, we see them holding hands and laughing together. This obviously isn't shown in the anime but it's suggested by the writers that they are more than friends.
Now, about the relationship between Eren and Mikasa in the second season. It's obvious that they like each other very much, and there are hints that they may be more than friends. But since the series is based in reality, not fantasy, I don't think we can say for sure whether they're just friends or not.
However, what is certain is that after Eren is transformed into a Titan, he and Mikasa break up. They don't talk for several months after this incident, so it can be assumed that they didn't have good feelings towards each other. But later in the series it's revealed that they might have met again after all!
Though readers may be sad that Eren and Mikasa are not reunited, Eren finally expresses his genuine love for his adoptive sister to Armin in the last chapter. Mikasa has never hidden her feelings for the boy who saved her life, and she has been working hard to repay him ever since. In fact, she has been so determined to make him happy that she has refused to feel any romantic attraction toward anyone else.
Mikasa knows how much Eren cares about fighting live humans, so she did not want to hold him back from this important mission. She also knew that he would be able to fight better if he was not focused on themizing themselves after a parent or friend. This is why she asked him to dress in civilian clothes when they went out into the world so that he could focus only on their battle with the Titans.
However, despite all of this, Mikasa still loves hearing Eren say that he loves her. Knowing this, it is no surprise that she wants to keep living so that she can hear these words again and again.
In conclusion, yes Eren does love Mikasa.