I really like all of the various teleport/transport options, each forming its own sub-network for getting around. It almost becomes a small game in itself: figure out the optimal route from point A to B, using a creative combination of transportation types. Granted horses (one of the best DDO inventions ever?) make it less of an issue, but the world is big enough travel time is still an issue.
The obvious ones include the teleporter portals, the airship network, Teleport and Greater Teleport spells. Another overlooked one is using Farshifters to create further shortcuts, like getting back to the far side of the Harbor from the Glen. If unifying Permanent Teleport Destinations for an account is generalized, as Lynnabel implies under the Saltmarsh release thread, it almost becomes another mini-network, depending on purchases. If this frees up the need to carry keys and bottles and whatnot that are needed to activate the teleport, so much the better.
This brings up two suggestions from me.
First, make access to Permanent Teleport Destination from older expansions, preferably as something you can earn in-game, or even just an item you can purchase in the DDO store. There should be a delay following the release of an expansion with one of these teleport destinations before one can obtain it - 6 months, a year, whatever. That way people who purchase it get something valuable for their money, like the way Universal trees are handled.
Second, link the water transportation network! That way you can go to the Harbor and not just travel to Korthos and Sharn, but IQ, House D docks, House K docks, etc. And vice versa. Some wilderness areas, like Ataraxia, Three Barrel and Sorrowdusk, could be better but not universally serviced, like an airport at a smaller city. Maybe the shipping lines that service this network eventually expand to include Saltmarsh as one of their ports of call.
I have no idea if this is a difficult modification, but it would increase the immersiveness of the city environment plus create another nice way to get around. I've always thought it odd that there's these various port facilities in Stormreach and Sharn that don't seem to have much use beyond that provided by a neighborhood bus stop.