Many of those examples are what I mean by players giving up at the first sign of adversity. #2 is something that is mostly a problem with the sand village which can be attributed to their only entrance being 5 tiles wide and right behind their casual hangout spot. The rest of the issues you bring up could be counteracted with gaining all 4 dailies at once, being able to progress through multiple at the same time. For example, if you are grinding snakes to clear the lair and defeat someone who tries to gank, you can progress on waging war by defeating them. For the issue of duplicates, there could simply be a system in place to prevent someone from gaining a mission they already have to complete.
Also, I agree that some missions exp rewards do not match the effort to complete them. Such as samurai drink/danger dangos which are essentially stolen documents for lowbies. These are additional issues that should be looked at and tweaked.