Someone bashing Skyrim recently (Not on these holy forums of course...) pointed out the fast travel and whatever how lame and whatever it was, but he also mentioned that if the fast travel had some sort of random encounter chance it would at least seem more belieable rather than a magic dragonborn amulet which teleports you arround. Could something like this be even probable as a mod? It sounded really cool in fact

So it would be sort of like Morrowind's sleep interruption chance, where there's a percentage-based chance you'll wake up with a random leveled (based on region?) creature around you. Or perhaps like old Fallout where there's a potential random encounter of any sort at random point between you and your destination. In any case I would play with that as a mod to remove a bit of the tedium it can cause when you go to and from common destinations with FT.

A wild bandit appeared!

Something like this?
http://skyrim.nexusmods.com/mods/12452

I don't remember this happening in Morrowind. Are you sure you're not thinking about a mod? Or perhaps you're thinking about the Dark Brotherhood attacks that added by Tribunal?