I think this is a subject with discussing, and I'd like to kick-start it with what we know:

1) Aleu stayed with Balto and Jenna over a year after the rest of her siblings were adopted.

2) Balto has this incredible journey with Aleu that he never replicates (that we see) with his other pups.

3) He refuses to tell Aleu that she's part-wolf until he's confronted about it from her; however, as seen in Wings of Change, Kodi at least knows about it (though when he found out is not clear), and it's safe to assume his other pups know about it as well.

4) Even when Aleu FINALLY realizes that she has found a new home, Balto finds it hard to let her go. He was less hesitant to let the other pups go (though he did show hesitancy, it wasn't nearly as much).

Considering these facts, it's likely this situation is a mirror of what happens in real-life. Typically, pups don't gain a connection with their parents (or siblings) until they are around 10 weeks old. This is why they are given out to new homes when they're around 8 weeks: they no longer are dependent on their mother, but they have not yet developed a bond, either. In the movie, we see the pups going to new homes when they're around 8 weeks old - the optimal time, just as in real life. When Aleu didn't find a home, she stayed with her parents, thus allowing a deeper bond to form between her and them, than it would have been otherwise.

That alone would make it at least plausible that Balto favors her over the other pups - though it goes without saying, if Balto was a good father, he loved his children equally, and thus simply favors Aleu instead of loving her more. In other words, while he doesn't love her any more than the others, he is more protective of her than the others.

Based on dialogue from the film, it's likely Aleu spends an equal amount of time with Jenna and Balto (Balto heads to Jenna's house after Aleu ran away, hoping she would be there, indicating that she goes there often enough for him to think that). Since she has no other home, she doesn't have a job, or a family to take care of her, so she spends time playing with Muk and Luk and Boris, and likely some quality time with her parents. It's logical to assume that she spends more time with Balto than Jenna, since Jenna DOES have an owner who takes her places ("My girl and I are going for a picnic today"), but Balto DOESN'T. He has free time, Aleu has free time, mix it together, and chances are Balto sees Aleu more often than Aleu sees anybody else. Psychologically, the more time you spend with someone, the greater the bond brows between the two people. 

(Note: we only know what eventually happened to Kodi: he got a job that often took him out of Nome. Whenever he sees his parents, it's usually only during breaks or visits. We know two of the pups went to the same home, and Dingo went to a separate home, but in the end we don't know what happened to them, or how often Balto and Jenna visited them. At this point, any kind of interaction between them and their pups is speculation, although it's also logical that Aleu would have visited them a lot as well.)

When Aleu ran away, Balto assumed she would calm down and return, evidenced by his dialogue in the film. This could either be simple ignorance, or he had enough faith in his daughter to believe that she would calm down and accept the fact that she was part-wolf (which she did, just a LONG time later than he thought). And then, when he decided to go after her, he went through several difficulties and bizarre events (raven, anyone?), but trudged through it because he loved his daughter that much. (Again, he loved his other children the exact same, and would have done the same for them.)

In the end, when Aleu finally found a new home, Balto was obviously saddened to finally see her go. He even mentioned how hard it was, and actually shed tears when she left (something he did not do for his other children). At this point, you finally see just how much they care for each other: Aleu embraces her wolf heritage, something she personally held against Balto previously, and left to lead a pack despite knowing it would likely mean never seeing her father again. Balto, who was reluctant to let Aleu go before (Boris observed as such), finally lets her choose her own destiny. I think, at this point, Balto and Aleu learned that true love meant letting go, no matter how close you are.

After Aleu left, we saw evidence that Balto had moved on. (Cue Wings of Change.) He goes on a new adventure, this time with Kodi, and is seen having a very deep connection with his son - which strongly indicates he held such a bond with his other children as well. It's quite evident from Balto's flashbacks that he spent quite a deal of time with Kodi while Kodi was growing up, but he seems to be a little more unsure of himself when it comes to meeting Kodi's expectations. ("You don't have to be a hero.") With Aleu, he seemed to not only be sure of himself, but more than willing to rise to the challenge of saving her - though granted, it was her life at stake and not her job.

In conclusion, I think that, while Balto loved all his children equally, Aleu was his favorite, due to the nature of their relationship. Hopefully you enjoyed reading this, and maybe it even gave you some insight!