Orochimaru's Hideout was so much more interesting in the show. I also think that your Jutsu Preference should affect more then just fights, so here is my idea.
Orochimaru's hideout is made much larger, and with disarmable traps, but only for certain people. There would also be several branches, so, for example:
You enter the hideout and the door swings shut behind you. You proceed forward, and soon come to a three-way split. You hesitate for a moment before setting off down the path on the left. You walk down the empty corridore, thinking that this is too easy... *snick* . Before you have a chance to turn and see what happened, several senbon shoot into you. You feel poison flowing through your veins. You need to run to make it back to the village in time to get the antidote. To heal this poison yourself would require knowledge of Medical Ninjutsu. (10 Skill points in Medical Ninjutsu are required to proceed)
Now, everything up to that point is filled in next time you come, but suppose you dont like Medical Ninjutsu, simply take a different route.
You enter the Hideout and hesitate slightly before heading down the central corridore. Suddenly the hallway is filled with impassable flames. A weilder of water Ninjutsu would be able to put these flames out ( 5 Skill Points in Suiton Ninjutsu is required to proceed) And so on...
After you pass *insert trap* you come to a two way intersection. You head off to the left. Soon you come to a plain wooden door that leads into a small room filled with various chests, boxes and barrels of supplies. You have found one of the Hideouts several supply rooms. Rummaging around you find:
3 Shuriken
2 Poisoned Kunai
500 gold
You hear the alarm suddenly go off and think it a good idea to leave before you are found
So there it is... thoughts?