If you look at history, what you have is:
1. VON 5/6 flagging (every single time you wanted to run the raid) was eventually removed.
2. Flagging for Desert eventually was removed.
3. Flagging for Restless Isles, eventually able to bypass with guild ship.
4. DQ flagging (every single time you wanted to run the raid) was eventually removed.
I don't know when the right time is, but it will happen eventually, using history as a judge.
I have bigger issues than the flagging quests (they can easily be whipped through quickly on casual if you don't really want the decent XP and favor they give). My issues are:
1. I want to be able to teleport (regular spell) to House C and Eveningstar (what ever happened with keeping teleport up to date?).
2. Guild ship teleport to House C and Eveningstar.
3. Key to Eveningstar - This thing if you click and so much cough you have no chance to reactive for an hour, and your teleport is gone. And why the hour timer? And why the standing looking at it countdown? There is no "story line" for any of this, and every time I see it makes me feel like someone is poking me in the back with a toothpick. Its a completely obtuse design implementation, at least for the player experience.