So, the eagles theory.
- The eagles were only doing Gandalf a favor for his saving the life of the lord of the eagles (not Thorondor) when they helped the Dwarves and later rescued him
- The eagles were always said to be interested in protecting animal life from evil, but how far they go in this is never really explained beyond their killing of goblins
- Tolkien was never definite about the Eagles status in his own writings, let alone including them as main characters in his books
The Eagles were used as a means to help the story along. It is not a plot hole. The eagles are an example of goodness in a tale of good versus evil.
If the eagles were to simply fly everybody around all the time whenever there was any kind of need… all of Tolkiens books could fit into a 10 page booklet.