Yes.
If you want consequences, random encounters and the like, don't use fast travel. Walk by foot.
Fast travel exist to skip over events like this.
And how you think character exactly travel during fast travel?
He is not magically teleport form place to place, there is large difference in used game time by travel by foot or ride horse and in FT also, so logically thats character travel in background on map and does not encounter of any enemy during this traveling, don't catch disease during travel and even more restore health and magicka during travel in wilderness, but encounter enemies during normal travel, I see there is something strange does not?
Another thing Skyrim has Holds and there will be Civil war, where is war there is front or border do you think character can easily FT between two rival fraction cities without consequences?
Fast travel in Oblivion style its almost the same like using console commands for traveling, using console for helping self in game is cheating, in such cases Levitation must also be added to game as legal replace TCL, or tdetect as legal replace for 100% chameleon and tgm and kill for 100% reflect damage and so on.
It also looks wonky and stiff, and the turning is just... weird.
Devs should make something much more, which isn't that easy...
Modders doesn't have full access to engine like devs have, many features beyond of us.
This isn't how it should've work in modern games...
I'm not demand carbon copy out Daggerfall, new tech allow make Carriage in realtime in better way
http://www.youtube.com/watch?v=yMhyeeasxkk