Currently, map travel costs are based purely on your current location.
However, many of us saves money by using PvP->Mist->LA->Closest city->Closest Asuran gate->Final destination.
I personally had not travelled directly from place to place since forever. For example when I am going to Ascalonian Catacombs, I would go PvP->Mist->LA->Black Citadel->Closest Asuran gate->Ascalonian Catacombs.
I believe travelling should be based on your current location and the closest city, to save us the headache. A few things:
1) Travelling to any city should always be free, from anywhere. - Let's say I am in Blazeridge Steppes. Travelling to any Asuran gates inside Divinity's Reach should be free.
2) The cost of travelling will be lowest amount based on your current location and the closest city - Let's say I am in Blazeridge Steppes (BS) and I want to get to Queendale. The cost would be based on from Divinity's Reach to Queensdale alne, because it is the closest city around and BS is nowhere near Queensdale. On the other hand, if I want to travel to Plains of Ashford, the cost would depend on whether the Black Citadel (closest gate) or my current location in BS is closer.
3) Fort Trinity (the Asuran gate inside the fort) will be added to the list after the player unlocks it. - That means travelling to Sparkfly Pen will be cheaper once the player unlocks the fort. This also means as the GW2 map expands outward (in future expansions), the player's travel costs will still be kept within reasonable amounts.