How did it appear?
You could make it mystic based magic. Make it uncontrollable. It could be attracted by massive sacrifice, prays, a death of someone significant, or other events. Noone knows why magic decided if someone was important or not, it just happened. Before anyone thought to examine it, most of magic was already used. People usually picked caves, forests for their templates so it will explain why portals formed there.
Is there a method / reason for how two portals connect in very different locations? Magic power would concentrate in those places, and randomly connect to places with same density of power in another place. It might require both spots to be created at the same time, to create link. This way you could have alot of portals without exit, entering such portal will cause anihilation of adventurer.
Grow and die. With time, magic could spread, lowering the stability of portal, at some point, loosing the link with original exit. It might change it's destination to another portal without exit, with similar density or it might turn into a trap. Decay process might be speed up by usage, so group of travelers entering unstable portal might end up in different places of world. Some of them might even die.
World getting older. In the beggining there was alot of roaming magic, so portals were created all the time. With time, most of it was concentrated into existing portals. This means, there is little to no unused magic to create new portals, making people believe that gods left them. Rarely new portal would appear if old one dissolved somewhere near.
