I was thinking when I was training--it's a bit boring to simply "hit a log" and gain the stat points you need. Fixing the system can be done using a couple things already included in the game.
1) Add Hp/Chakra to the list of options when spending points. 1 point could be equivalent to say, 50 hp or 5 chakra. Implementing this would allow players to build up their HP and Chakra using the hard earned points.
2) Remove logs, Keep mission training. This would make training slow at first, since players would have to start @ D-Rank on the mission ladder and wouldn't be able to handle tougher missions until they've worked at it for awhile. As the player gets stronger, training would become gradually faster due to being able to handle harder missions.
3) Flesh out the mission list a bit. Instead of keeping it at JUST 1 D/C/B/A/S/SS/SSS mission, extend it. For instance, instead of Weed Picking for Rank D, you could choose to do a D-Rank "Sparring with the Sensei"mission, or "Deliver the Ramen to the Hidden Grass" mission in D-Rank. There's a ton of possible ideas, and the more variation in missions, the more likely people are to enjoy mission training. Aside from NNG rips, very few games have a well-done mission system, so it's something new.
Sure, this would probably mean a wipe, but it'd also be more balanced, fun training. Win/Win imo.
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