I think there are two discussions going on and mixing in a confusing way:
- fast travel vs no fast travel
- waypoints are immersion-breaking and should be replaced by implied walking (as a fast travel flavour), which would mechanically be the same, but improve immersion and not make one question the game's worldbuilding
I believe the OP wanted to discuss the latter and few people are calling for removing fast travel altogether. Although I must agree with Tuco, especially on the "games should be designed as if there was no fast travel and then fast travel should be added on top of that system". That way playing with no fast travel is viable and one can judge whether he needs/wants the extra convenience.
On the "walking" front, +1 to what mrfuji3 wrote.
