What's needed is a far simpler waypoint (WP), selectively (and probably) densely placed in regions, their positions determined by:
-Value of location and corresponding risk. Fast travel eliminates (skips) risk. Some areas ought to be dangerous i.e. a high level quest points you to Voldemort's tower, which is past the Prarie of Apocalyptica. FT allows you to skip the Prarie just because you've been there once on a different errand. The solution is to place the WPs somewhere near the outskirts of the region.
-Immersion. Quite possibly another level could be built on the waypoints whereby some WPs are commercialized and so cost gold to activate; some are restricted exclusively to certain factions. As a compromise, WPs only work within the same nation (or whatever the term is) and so the player is required to take public transportation to reach the capitals of wherever before they can reach the nation's WPs.
-Tedium. Morrowind's system, with some destinations NOT available at all Silt Rider locations, resulted in much tedium. Now clearly the system could have worked otherwise without any corresponding drop in realism.
-Design. Instead of taking a universal approach, why not tailor different systems for different scenarios? For example, some quests may be based on exploration, whereas some may be highly intense, tightly scripted affairs: less/sparser WPs may be conducive to the former; the latter would necessitate generously placed, easily accessible WPs.
Edit:
"fast travel only breaks immersion if you use it. You are not forced to..."
I don't think so...games should always take charge and dictate. It is human tendency to resort to the easiest course. Presenting options for systems that greatly diverge the game experience is, in my view, a bad idea.