Fast travel is one of those game-mechanics I really like, along with things like awesome player homes and amazing companion NPCs. However, player homes and companion NPCs are something made more enjoyable by the fact that they need to be earned in some way (most appropriately through relevant missions/quests). I think that Fast Travel could be enhanced, as a game mechanic, if it only became incrementally available through an optional system like perks. I think http://www.gamesas.com/topic/1576744-little-things-that-annoy-you/page-7#entry24799038 by @Hoblak is a great way to make the whole Fast-Travel experience that much more meaningful and enjoyable:
I would suggest that it really is a good idea to keep something like Fast-Travel optional at different levels to suit different styles of play and it is an even better idea to make Fast Travel progressive to help vary play as the player character levels up.
Having said this, I would have thought that something like Fast Travel would revolve around perception and endurance because one needs to be paying attention to stay out of trouble when operating in less than "savoury" areas and the ability to stay on the ball when travelling depends on us not becoming too fatigued to do so - which is endurance-related. Of course, sometimes not being noticed is just a matter of looking the part so, it could also be argued that charisma is the Fast-Traveller's best friend.
This is just to say that, in terms of accommodating other suggested additions to the perk system, I think there is a lot of room for flexibility when implementing a Fast Travel perk
Moreover, one thing that is problematic with the perk system is a lack of flexibility attached to having a full perk table, which makes perk-related mods somewhat more difficult to accomplish. Having gaps amounting to, say, 25% of the perk table, in a system where S.P.E.C.I.A.L. attributes max out at 16 would make room for update and DLC additions to the Perk system while allowing some space for modders to introduce new perks without displacing existing options and mechanics.
There are several suggestions in extant, which are dependent to some degree on additional perks and I also think it would improve the longer gameplay afforded by the Fallout 4 world if the S.P.E.C.I.A.L. system could be extended from 10 to a nice round number like 16 (i.e. giving 4 bit attributes).
Food for thought,
bon appétit!