I too would like to get more directions in the jurnal but I can live with most of the marks. Imagine it like "go there do that, here let me mark the place on your map".
Yes, always pointing the NPC in a city/building/room is immersion killing, that I don't like even with what I sayed before.
Even a bigger problem is the example with that book you get a marker when the NPC just tells you to find one, I actually found a different one, unfortunately after I finished the quest so I can't tell if the quest could have been done with another book of the same kind. For this and the NPC finding situation a dialog with NPCs around cities to tell you it the one you look for is in the city and where would have been the nicest solution imo.
About quests you don't wish to do...I would be fine with them stuck in jurnal but at last give me a hint about something like the alignment related to that quest (like kill an inocent/kill a bad guy)
Now the unusual gems thing...that's actually bad design but has nothing to do with quest markers, it's a different thing. I didn't ran into this issue, I wished to join thiefes guild and found first gem after I did. But I had a similar story about me joining the mage guild...see my spoiler if you wish, (I'm really curious if I could do what I had to for other quest without joining the mages).


