There are three eagles simply because there are three characters being carried:  Gandalf, Frodo, and Sam.  Gandalf is there to guide the eagles, as he is probably better equipped to locate the ring bearers than anyone else.  Keen as the eyes of the eagles are, they are not (as?) familiar with the Frodo's mission and so would probably not know where to look to find the two hobbits.

Gwaihir cannot easily carry one of the hobbits himself, because he already has Gandalf in his talons.

>'Twice you have borne me, Gwaihir my friend,' said Gandalf.  'Thrice shall pay for all, if you are willing.  You will not find me a burden much greater than when you bore me from Zirak-zigil, where my old life burned away.'
>
>'I would bear you,' answered Gwaihir, 'whither you will, even were you made of stone.'
>
>'Then come, and let your brother go with us, and some other of your folk who is most swift!  For we have need of speed greater than any wind, outmatching the wings of the Nazgûl.'
>
>'The North Wind blows, but we shall outfly it,' said Gwaihir.  **And he lifted up Gandalf and sped away south**, and with him went Landroval, and Meneldor young and swift.  And they passed over Udûn and Gorgoroth and saw all the land in ruin and tumult beneath them, and before them Mount Doom blazing, pouring out its fire.

In *The Hobbit*, Bilbo and the dwarves were able to ride on the eagles' backs when the mounted up under safe, controlled conditions in the birds' aeries.  However, when spontaneously picking up someone from the battlefield, the eagles must carry them in their talons.