As in, rare and randomly occurring in the world rather than created by the player. I have no idea why I'm even thinking about this because I'm not even up to portals yet in my game, but I've read some of the threads about it and this idea keeps coming back to me. I think this could eliminate a lot of the current issues with portals – they wouldn't be an infinite player-created resource, but could still help you get around, depending on where they are, where they go, and when you find them (I have no particular opinion about whether you could transport ore between them).
There could be a portal near your spawn point, or not. It could go somewhere useful, or not. You could choose to build near one, and it could help you access faraway resources, but you might have to learn the layout of the portals in your specific world to get where you want to go, and you'd probably have to do some adventuring and exploring when you got there rather than jumping straight from base to base. Perhaps portals in dangerous places would be guarded by enemies, so just jumping through the first one you find at a low level could be a risky proposition. Perhaps they might even spawn in dungeons from time to time? Maybe when you got to a high-enough tech level you could gain the ability to re-map existing portals to make them slightly more useful (rather than make your own from scratch). I just feel like this could add a lot of excitement to the exploration of the world and perhaps some variety and replayability too. I know I've read the devs say that portals are not changing, but is there a mod that does this or something like it?