Okay, this is so obvious, I'm pretty sure someone is already working on it - but I'll be specific.
1. Quests can be sorted by area if you select it to be so.
2. Ability to drop quests that go stale.
3. Quests automatically track a certain amount of hints and directions, rather than simply having to remember every word some NPC gives, because you can never read that dialogue again (especially annoying on mobile phones, because accidental taps happen). This is critical for me.
4. Quest reminders pop up when you are near something important (though you should be able to turn this off, and maybe having it on reduces experience and/or gold).