I have mixed opinions when it comes to quest markers. For the most part I tend to be in favor of them as conceptually it shouldn't be difficult to find what your looking for in most cases, and really nothing turns people off faster than wandering around lost for an hour or two trying to do something simple or that should be obvious.
That said, making the point of certain quests being to find something based on directions is also quite workable, and of course in cases like that there shouldn't be much in the way of guides. Likewise as "The Secret World" demonstrated with it's "investigation" quests, there is nothing wrong with creating quests that the players need to figure out themselves.
When it comes to exploration, I think the problem is mostly that game developers are lazy when you get down to it, that's why most games tend to involve a situation where everything is connected to a quest, and you get sent following a marker to every point of the map at one time or another. Ideally in developing MMORPGs, in addition to the areas that quests take you/lead you to, there should of course be plenty of additional space, and of course game developers need to put things unassociated with quests out in some of those areas to encourage people to engage in exploration. For the most part doing things like that takes work though, and game developers don't want to put that in. Especially when you consider the content they generate that way will probably be missed by a lot of players (unless they hear about it second hand, or by visiting websites or whatever). This was one of the big reasons why raiding became so casual in a lot of MMOs, before that big changeover I was hearing things about Devs whining about putting tons of time into developing high end raid content that was only ever going to be seen by a relatively small percentage of the player base, the idea being that if a developer puts work into making something, they want it to be seen and played. This was part of the equasion a lot of elitists (which has included me) tended to miss, and still continue to miss to an extent, part of the whole "content for everyone" movement and "endgame is an entitlement" which creates problems in of itself largely comes from Devs who don't want to spend thousands of hours developing and testing something only 1% of a given player community will ever see.
Overall I tend to think "The Secret World" had the best ideas of any MMO ever on how to do quest content, as it had a your typical "someone sends you to the marked area to kill everything" quests, it had mob avoidance quests, and it had puzzles which even expected people to look things up online to solve them (The Secret World even has a button to easily open Google within your browser). As a result it wound up with a good mix of content for both relatively "noobish" players and more elite ones, and reality being what it is eventually the solves make the rounds so in time everyone gets to see everything anyway, but the elite can usually come out well ahead of the curve.