What's the difference if you click on a location on the map and fast travel there or if you pay for a service (like boat or animal) and travel there. Either way you're getting "teleported" to the location.
- You have to be at the place or travel to it first before you can use the fast traveling service. Rather then being anywhere and fast travelling from that spot.
- Usually the travel services only transport you to known locations, cities and the such. Rather then being able to fast travel to anywhere in the world.
- You have to pay to use it so there's a sense of I don't want to do that always. Rather then oh it's free why not use it.
Personally I like the way World of Warcraft does it, or the way Morrowind was. Where you have to pay for the ride and the ride only takes you to other cities. Plus it's always cool to ride on the backs of cool creatures like Gryphons, Hippogryphs, Wyverns, Giant Bats, Dragonhawks, and of course the ever awesome http://farm4.static.flickr.com/3200/3134862056_71f2bfa875.jpg.
I would think the Radiant Story random encounters would be better utilized in a system where you actually had to walk from town into the wilderness to the cave or wherever your going. Walking through the forest and all that is how you level up, where the action is. Rather then fast travel and skip it all. You would hardly ever see the random encounters in action then. A fast travel between cities system is a good idea though. Cities should have roads between them, or at least trails. And then Skyrim could have a fast travel or taxi service between them, via horses or something.