It changes the god/cleric relationship. In 1e, 2e, and 3e, you were intended to meet and perhaps even fight gods and avatars. Gods also provided spells and could withdraw them if they so chose. In 5e most adventuring clerics go because their god told them to. Now, the class does mentions some non-cleric priests that have no communion with a god, but those aren't true clerics. In 5e you know your god exists, you know his will, and you get direction from that god or else you couldn't go adventuring at his command.
What is says is that in 1e, 2e, 3e and 5e gods made their wills known directly to their clerics as a matter of course. Eberron changed that by removing gods from direct communication.