Fallout had good fast travel. You still had to explore the world while traveling to the location, possibly stopping on your way to acquire new items/whatnot and then once you made it you could travel back there instantly to save yourself some time. In addition you could add Mark/Recall spells, Intervention spells, an unique item that would greatly boost speed (similar to Boots of Blinding Speed), though I doubt levitate/jump/free fall will make it back, and maybe different travel services as well as fast travel. That way the lazy have fast travel while those looking for immersion have options to chose from beyond fast traveling and just normal walking.
For quest waypoints:
Highlight the general area on the map where the the objective is, perhaps with a faded red circle or some other indicator. Morrowind did not do anything like this and some quests were just impossible to figure out. So you have an idea where to go, but not the exact details. So you must explore a little. Nothing pissed me off more in Morrowind than walking in circles for hours just to find a hidden cave for a quest. In addition, the NPC's could have Morrowind description with a psuedo-Oblivion waypoint... just a general area, not a specific marker so exploring is still possible.
For level scaling:
Most people want it gone. In my opinion it should be 50/50. I want certain enemy type to scale with you. This way certain enemies will still pose a threat, while others like mudcrabs will be easy to slay at higher levels. Maybe like Daedra lords, a specific type of bandit, major NPC's, and what not. While on the other hand you have a majority of enemies that you can't overcome till a specific level, and enemies that you'll crush once you are a high level. Perhaps have the weaker enemies gather closer to towns and the stronger ones be out of your way...