As for fast travel and quest markers, if like in Oblivion, the quest designers "Suppose" that there is a "Fast Travel" system, and "Quest target marker" that "Everyone" has to use, because there is no "Alternative", then they do not feel that they have to give "Adequate" direction, and they do not feel that they have to think about the "Route" that the players have to find and use, so the end result would be that they "Suppose" that just "Marking" a point in the map and giving the quest target a "Target marker" does the job and skip "Giving the adequate directions by the quest giver", and "Supplying enough noticeable landmarks and direction helpers in the route".
Which results that you can not say that it is optional, just do not use it, because if not used, you have nothing to rely on.So the better option is if they want to supply fast travel and GPS markers, they should suppose that some people might not want to use them and give adequate original directions and route finding helpers.
In Morrowind, I really loved to use my tracking skills, and look around to notice small things that would click a direction in my mind, so looking back at the quest notes to find a line that could help me with continuing , and in doing so, and without the teleportation mechanism supplied by Oblivion's fast travel, I would find a lot of small details and occasional surprises in the route that would not be found otherwise.
You have to walk a direction,
+ you have to look around keenly for signs,
= you find a lot of new things in the way.
In order to accomplish "true quests", I'd say:
1) Get rid of quest markers for "normal quests", add voice-acted directions/hints instead. For randomly generated quests, add a "Let me mark it on your map" dialouge so that it doesn't get too expensive for Bethesda with all the voice-acting.
Optional area marker is not a bad thing, so they mark a general area/cell and say that in this place, but when you reach that place, you have to find the target yourself, for instance, if you are looking for a sword in a house, you should look where such an item might be, in display cases, or closed/locked chests, and so on.
Or if you are looking for a person in a town, you could ask people about him, and they might know him and tell you about his regular activities and where-abouts, and when you could be sure to find him and a specific time, and the like. Some might be able to point him out for you, if he was in sight.
Daggerfall style, "Go north west from here" should also return, or even something like this:
As for another instance, we can have a lot of guide object scattered through out the landscape, scripted to help local NPC AI, but some of them can be as land-marks to help NPCs give the player character correct addresses and routes to a destination.
So when you ask an NPC if there is a monastery around, the AI can communicate with the local search engine and supply it with the subject of your conversation, currently a monastery, and wait for the result, as the NPC, stands still holding his chin in his hand and saying, "Hmm, let me see...".
Then the search engine finds the needed object, and gives back a list of the land marks in the route until it reaches the subject of the search, i.e. the monastery, and the NPC responses, note that I would underline the landmarks and guides:
"Yes, there is one, but you are for a bit of traveling. You should go along this alley, until you reach the fork, then turn left and continue until you reach "The Village Center", then you should follow the road toward the river, until you reach a big building with a fishing boat sign.
Go inside and ask for a ferry, and tell the ferry-man you want to go to the "Bubbling Bay", and when you reach there, look around for a nearby bridge and cross it, then you should continue toward the forest and at the edge of the forest is the nearest monastery to us."
2) Add puzzles, riddles, touch choices, tough enemies. Sometimes the quest should be so tough that you have to try again later, or use your super-pro-skills and work really hard and still complete it.
Should require some looking around, searching through book pages, asking NPCs around, sneaking past, outrunning, or avoiding powerful enemies, or coming back when you can finally beat them, looking up toward ceiling, or searching the ground, deciphering runes by the help of books, moving objects around to help you climb, or block enemy routes, or to put weight on trigger plates, and the like...
3) Some quests should challenge your strength (tough enemies), some should challenge your wit (need to think a lot), and some should challenge speed/agility (stealth). Add some moral choices as well.
Perhaps even one single quest can be completed in different ways like these.
Yes, all the archetypes, (Fighter, Mage, and Rogue) should have equal opportunities to solve quests in their own distinct ways.
Don't let quests be some robotic, static approach, where you just do what the NPC told you. Of course I don't mind a few quests to be like that, but... as I said, only a few, for variety's sake. Let most quests force or allow you to think.
Things shouldn't be like:
1) talk to NPC,
2) go get item or kill NPC,
3) return to NPC and get reward
Yes, no pampering and hand holding.
I completely agree with what Spaghne and Merari said.
And I with you.