When making a RPG, one common flaw is that the developers never seem to play the game. This is attested to by the awful methods of transportation in some RPG's on the market today. I'll give examples of good/bad games, then examples of good/bad systems.

Good Games-

1. Oblivion: Quick travel and mounts, though the mounts are more just annoying, as well as potential level-up speed increases.
2. Morrowind: Level-up speed increases, freeform traveling (Flight from Seyda Neen to Balmora, now departing...)

    Why Oblivion is good: Oblivion combines a mix of speedy travel through a menu, wonderful scenery, and the ability to ride a horse or run really, really fast at high levels. Not to mention speed buffs.

    Why Morrowind is good: Morrowind has the ability to buff speed or run fast, like Oblivion, and features a wonderful custom item/spell creation system that lets you FLY! Ok, so not in the technical sense most of the time, but you can get really far really fast with custom rings/equipment and a spell.

Bad Games-

1. Oblivion: Annoying mounts, insane level design
2. Morrowind: No free quick travel, insane level design
3. Too Human: Baldur's Gait (thank you, Yahtzee), insane level design
4. Fallout: Insane level design, elevators
   
5. Baldur's Gate: Insane level design
6. Lionheart: Insane level design, quick travel

   Why Oblivion is bad: Oblivion combines a mix of quick travel with insanely large and complex levels, in which you are usually incapable of using it. Also, mounts tend to follow you whether or not you want them, often causing damage to the horse or your stealth potential.

   Why Morrowind is bad: Morrowind requires you to pay to quick travel. More, most people don't necessarily know the travel routes. Also, like in Oblivion, the level design is terribly confusing.

   Why Too Human is bad: Slow movement combined with huge levels is cool for the first half of a second. Then it gets annoying. Epic scenery is available, but it mainly disorients the player, and the level floorplans don't help. Having a quick-travel system that doesn't really take you anywhere is more or less pointless.

   Why Fallout is bad: The levels in Fallout are terribly complex and confusing, much like those in any good RPG, but the elevators also add pain. Repeatedly stepping in elevators or not getting in elevators or elevators not taking you to where you want to go is a frequent source of confusion.

   Why Baldur's Gate is bad: Baldur's Gate isn't bad, so to speak, so much as realistic. Cities are huge, and it doesn't seem like such a chore. The quick-travel works. But it's still incredibly confusing to navigate.

   Why Lionheart is bad: Expansive open levels are okay, but be sure you don't get too expansive so that the player gets lost the second he leaves. Teleportation is also disorienting. Also, using the blue crystals for quick travel has two drawbacks: Some people may never learn they're there, and also, they may not be in enough places, or in too many.

Good Methods-

1. Quick travel: Path of least resistance, but it allows players good amounts of freedom.
2. Mounts/vehicles: If you pull them off right, they can be both quick transportation and a useful piece of equipment.
3. Player-Orgin Flight: I admit a bias, but flying is quick and fun.
4. Level-up: Moving quickly is easy if you can choose to level it up. It's also useful for combat or whatnot. Works best in true 3d games.

Bad Methods-

1. Quick travel: May spoil the player, may also cause massive confusion.
2. Mounts/vehicles: They should not be dreaded.
3. Elevators: Especially if they consume a lot of time, elevators are not only boring, but often can cause confusion.