@Zaer: Trapping people in crystal, making walls of crystal, etc, replicates ninjutsu used by dozens of different characters; it's not some new thing, even if some of the flavours or particulars are unique. With a technique like that, it becomes who can play the best strategy using the tricks at their disposal. A reflex defence will work no matter how clever an opponent is; in a game where no definite measure of speed, reaction time of the technique, etc, it's the sort of thing that can lead to fights that can't easily be resolved.
Some comments on other ideas you presented:
The 'gut sense' strikes me just as bad as the crystal. It reeks of metagaming. Some way or another, he always knows what he has to do to counter someone. It raises the same issues as the diamond, as well; he'll sense an attack coming, no matter what, and will instinctively know the method of countering it, rendering the attack null. Even worse, it doesn't even require explanation, because it's just his gut.
I suppose my only issue with the water-purifier is that there's no conclusive method as to what he's doing. His one ability apparently functions to neutralize acids/bases, kills diseases, removes random chemicals and substances that effect the human body. It's too much a case of intelligent design without any particular purpose. Even the Sharingan's wackey-doodle list of abilities makes sense if you consider it a mutation or devolution of the Rinnegan, which was just raw power in the form of eyeballs. The big point to make however is that regular Water Release jutsu have displayed many of the properties you're describing, producing fluids ranging from water to oil to syrup. Im not sure if it's really worth making into a kekkei genkai.
Your jack-of-all-trades, jounin-level genin actually strikes me as a cool idea (admittedly because I don't need to make judgments on power level
). I would prefer a little bit of theme to the ability set; people have elemental affinities, and it's one in a hundred who actually use more than two. Also consider that using genjutsu effectively requires above-average chakra control and intelligence, while using most taijutsu requires above-average speed and strength. You can only push his natural abilities so far before he's just a Sue, but the limits of his techniques will be based on how strong he is in each area. Just be careful with the balance.
And if you have more ideas, please mention them. I wish I wasn't being such a joykill >_<.
@Elias: Don't forget the number of techniques the summoning trees often have at their disposal aside from senjutsu. Aside from a few creepy cases of body-mod, almost everything Orochimaru did was tricks taught to him by the snakes. Jiraiya was almost as bad for it, too. And I only assumed you planned on using sage abilities because you mentioned it in his etcetera, and that he liked to practice with them and try them out himself. I just wanted clarification if you were going to do so; while full sage mode would be a little extreme for this game, using it for momentary boosts and such wouldn't be harmful.