After doing daily missions for a couple of weeks, I have observed myself play less and less. As of right now, I only log in to finish my dailies, and then I log out until next reset. It is due to the fact of how the missions are structured. All the missions are independent, and have no correlation to each other. The journey to do those quests are tedious and not fun at all. To me, the missions are not ninja in any way, and are more like your standard mmo questing system. Taking all this into consideration, after all these grueling weeks of daily mission training agonizing, sweating, perspiring (I need a new deodorant), and finally conquering swampy ass, I have come up with a new jutsu!
Daily Style: Flowing Mission Jutsu!
The fact that we have a mission counter is excellent design. I want to expand the possibilities of this system, therefore I shall start by explaining the flowing part of the jutsu.
Picture this my dear reader.... "You're running full sprint towards the mission counter because it is almost time to reset, thinking that its going to be the same old, you talk to the mission giver, and lo and behold a new D-rank mission: Robber sightings". The mission giver explains that there has been an increase of Robber activity near the crossroads to the south of Leaf, and asks you to investigate. When you find yourself at the crossroads, you notice footprints that lead south. You click the footprints and that ends that part of the D-rank mission and gives you a box. Those same footprints give you the next quest D-rank mission: "Investigate the activites of the robbers". Now you go around the camp finding 2-3 different clues that give you a general idea of whats going on. After finding those clues, this 2nd mission is over, and you get another box. After that's done you get a mission item in your inventory, right click it to get a new mission.
D-rank mission: "Subjugate the robbers". You kill x amount of robbers and get other clues (tobacco shipment), and you start noticing a pattern (when you're done you also get a box). Many of them have tobacco shipment boxes with 2 letters inscribed on them HS (not sure if it was Hanzo Wasabi or not the name of the guy that deals with tobacco shipments in Kisaragi), and you also find a letter on one of the robbers detailing instructions to bring the shipments to the border between the Land of Fire, and the Land of Rivers.
This is how the C-rank mission: "The mastermind is unveiled?!" is bestowed upon you. Now you must go with your team to find Shiro Uchiha and stop his plans. Upon killing him(you get your box of course), on his dying breath he says something disturbing "You....have no....idea....what....to Leaf!". Upon inspecting Shiro's corpse, you find another letter that was supposed to be sent to the southwest to a "rogue hideout".
At this point you get the C-rank mission: "Discover the Rogue Hideout!". You being the tenacious ninja that you are, you embark on a journey to find this rogue hideout. When you finally find it, you resolve yourself into infiltrating this hideout to find any information about what Shiro said as his last words. Inside you will find a scroll detailing plans from an unknown individual that has set up all this situation to make many ninjas get out of Leaf Village, so that he can invade it from behind the mountains and destroy the leaf(you know the drill, give me that mission box).
After getting the scroll from the rogue hideout we are bestowed with B-rank mission: "Defeat the mysterious individual before he destroys Leaf!". After you defeat this mysterious individual (getting your box as a result), you notice a ring with a distinct insignia on one of his fingers. (This ring might give a hint about the next steps). After that you remember that on the hideout that you infiltrated there was a wall with this insignia painted. The ring will bestow the C-rank mission: "The Ring, the wall, a mystery to unfold!". After infiltrating and passing through the wall with the insignia (has to have the ring equipped). You find some treasure chests with some goodies (got to reward the effort), and on a table you find some documents that have to do about someone called Raido. UH OH cliffhanger!
This example presented is how I find a mission in Shinobi Story could be done. It has a backstory, and an unfolding story, making the player more immersed in the world. Secondly in terms of just the way to do a mission that flows with itself and doesn't make you do crazy detours to do 1 mission. Instead it keeps giving you missions along the way without having to stop, and at the same time makes you travel this beautiful world map Shinobi Story has while using elements of it to complete the missions.
For the rogues it can involve the same, but from the other point of view, making it so that both rogue ninja, and village affiliated ninja will see each other in the field while doing their respective missions creating conflict.
With this I finish all the hand seals required to manifest Daily Style: Flowing Mission Jutsu (my fingers hurt), and I sincerely hope to inspire the developers into creating an even better game, because even if we don't say it as much, we the players find this game is awesome and we want it to be the best it can be.