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Was it because of live action begin or that it is cartoon or made in the wrong time or that Balto isn't cute enough? Then theme of prejudice or a wolf dog hero or something like that?

Balto isn't what I'd consider a popular film due to a reason. None of which I think have anything to do with the live action beginning or anything else that you mentioned above. . :p I think it is due to the poor advertisement of the film. Not to mention they released it at around the same time as Disney's Toy Story, which was the first ever Disney CGI film. Toy Story overshadowed Balto, causing it to not do as well.

I LOVE Balto and I am glad that there are other people that love this movie as well.

I think it is considered for young kids.... the saga lost popularity a little while after the third film was released. This film is not as appreciated by the general public because many new shows and cartoons have emerged. It has limited following as it largely overlooked by the general public The film has a narrow following only liked among young children Sled racing in alaska is just not popular... after the third film, universal kids discontinued making more films for balto . There was hope for a balto 4 but it never came.
For example, A similar comparison of a cartoon saga that is closely associated with fans of Balto is All Dogs go to Heaven and its affiliated sequels , The popularity was high for this cartoon after in late 1990's. A second movie was produced and shown in theater around spring 2006. Later that year a a series was made featuring Saturday morning cartoons and various media such as action figures and a computer game was made making the cartoon interactive with fans. re runs of all dogs go to heaven the series went on for some time. The last film produced was the Christmas special ... there was re release of improved versions of the film saga with blu ray....

unfortunately.. much like balto. as time went one the saga's popularity faded into obscurity within recent time only being liked by young children. Popularity for All dogs go to Heaven is underground or online now

On a positive note, some live action movies have been released recently that explore the history the history of Balto with a live action film. One of them is the great Alaskan Race. The other is togo which explains the events of the 1995 serum run and how the musher went to get the medicine, togo comparable to steele is the feature character while balto his companion is also emphasized, they are companions instead of enemies. It shows how the journey was very hard. The movie is recommended.

I thought the same

It was vastly overshadowed by Toy Story as they were released around the same time. Very sad, really, since so much effort was put into this film.