Element's And jutsus redone

This is true but there could be a system implemented where you have to use some of the jutsu in sequence with your other moves For instance to gain mastery you can start off with any jutsu Such as for katon say i use Hosenka the game would generate and say in the text box "Use- Insert katon jutsu here <- it would be random among the jutsu you have unlocked in the element Thus making Afk training or spam training not possible

Like indigo, I also think that these ideas are not too bad. However, I think the flaw of your current idea for training jutsu mastery is that it makes the gameplay itself lean more towards a spam-grindy style for this form of training. If I were to add to this idea, I would think it better to make it so that the player is required to get KILLS using their elemental/profession jutsu with amount of mastery obtained being higher depending on who his killed. This would keep the gameplay and training style as versatile as it is while implementing what I have interpreted as the heart of your idea.
example:
killing rogues with fireball is +1 katon mastery.
killing rock lee with fireball is +10 katon mastery.
Killing sasuke with fireball is +30 katon mastery.
The values are completely arbitrary but you get the idea.