What I see is that at one point it was a free magic, you could learn the spell and go about it however you liked. But then certain mages allied themselves against the Empire and caused havoc and were traitors in some way, seeking after power. And once the threat of this kind of freedom was exposed, that spell was restricted to only the greatest mages in the world, those who were not only powerful, but have proven themselves trustworthy. Those who receive the spell must undergo a ritual that marks them, so that if they ever go rogue against the Wizard's Enclave of Tamriel, they could be stripped of power and removed from service as a mage for punishment of their crimes.
In the meantime, you receive Runestones that you can use to go wherever (whatever city) you like as long as it is to a precise location in the city you've chosen. I want to impress upon the traveller who is using Fast Travel this way how dangerous this power is, and how restricted it is, by having all the concepts of fear surround the spell's use. What I mean is this ... when you go to Fast Travel, you need to visity a Travelling Sepulchre. It's a half-moon crescent of glowing stone on the backside with an open front. But standing in the other spaces to complete the circle are a number of high-level Mage Gaurdians who are there to ensure the safety of the operation. They will ask you where you are going and record it in a log. You cannot travel during certain high-magical times due to the dangers of such travel, and you cannot travel from 12midnight to the morning during the Witching Hours. You click on the floor and a list of cities comes up. When you cast the spell, the screen doesn't just pause, but energy forms around your character (essentially the game engine casts a special teleportation spell on you that is cool to watch) and the magic keeps animating while the next scene loads which is identical to the one you left so that there is never a pause and with some cool "swooshing" noises you will feel as if you've travelled. When you arrive, several of the mages will scan you with their magic before you can proceed. If you travelled illegally, such as on the wrong day or at the wrong time) you must pay a penance and face a week suspension from learning any magic skills etc....
Now when you use the rune, it's gone, you have to ask for another one. But whenever you go to ask a higher up for a rune, they assign you a quest first. So say you wanted to travel from A to B to complete your current quest .... but before you could go to B, you first had to go to some dungeon and acquire some book that was lost there. After your quest, you are given a Runestone allowing you to travel back to B and complete that quest also.
Now, once you are of a certain level, and have proven to be trustworthy, then as a reward for your progress, you could be given the spell that offers full unrestricted travel between gates, although your comings and goings are still noted and recorded, and the game can use those dates and times to throw monkey wrenches into the plot, such as indicating that you were in a certain location the day an artifact went missing, can you prove you didn't steal it? So you go on a quest to determine who actually did, and recover it, clearing your name. That could all be Radiant Story driven very easily under that system.....
Anyway, what are your thoughts, given my reasonings, on Fast Travel as I have explained it?