Random encounters are very overrated. If you want travel to be riskier, then you can fast travel to one waypoint, jog to the next, and then fast travel to your final destination. You can even skip fast travel.
Random encounters might be good if our characters' abilities and choices are fully accounted for in the encounter determination. If the character can cast invisibility at will, and if characters do not need sleep, then the chance for an encounter should be zero. If the character has the Chameleon effect available from an item or a spell, then the chance for encounters should be reduced accordingly. If the character can outrun anything that can harm a running character, then the chance for an encounter should be zero. As a character visits a location multiple times, or travels through particular regions multiple times, then his growing familiarity with the routes, and with the possible dangers along them, should be accompanied by a growing reduction in the chance for encounters. What exactly is encountered should be determined based on the likelihood of encountering such a thing, and if such a thing poses no threat that character -- based on the assumption that the character will seek to avoid combat with it -- then the encounter should not happen. If you choose to travel cautiously or recklessly, then the chance for encounters should be appropriately adjusted.