Re: Shugenja
I want to echo what others have said about shugenja mechanics and add a few thoughts of my own. Firstly, there is little about the current incarnation of shugenja that I'm particularly enamored with. I like their school techniques that give them a little flavor (as opposed to 1e when they were all pretty much the same). Likewise, the magic system does need a major overhaul. 4e carried on the problems of 3e where shugenja were simply the best at everything. I understand that at times the system was not designed to be perfectly balance, and that is okay. However, when the gulf between your weakest rules and your strongest rules grows too wide, then you have completely broken your system. A small difference in power-levels between mechanics is fine for any system.
That said, spells remain one of the major offenders of the system. I agree that shugenja should focus more (not exclusively) on the supernatural aspect of the setting. I believe that is where their power should lie. An oni was summoned by a maho-tsukai, this is the shugenja's time to shine. Meanwhile, out on the field of battle, perhaps only the most powerful shugenja are able to truly play battle-wizard.
If anyone is familiar with the Qin RPG, they have a wonderfully balanced magic system that evokes a Taoist flavor with internal alchemy, external alchemy, geomancy, divination, and exoricsm. Now, I know Shugendo (the religion Shugenja are based on) and Taoism are very different, but the point is that even though at slightly higher levels of power the magic user is able to fly, and hurl elemental forces, these are very limited and costly effects, but which, at the highest levels of power can be extremely potent (though draining) abilities. Meanwhile the lower level abilities are very much in line with the supernatural and subtle forms of magic.
Get rid of Mastery Level, and keep all spells at a specific level of power that will, of course, increase naturally, over the course of character progression. Your starting shuggie can have that Tempest of Air, Fury of Osano-Wo, or what have you, but have that be the single spell (much like bushi have weapons), that are then improved upon as shugenja get better at casting them, rather that being obsolete as shugenja gain ludicrously more powerful versions (Slayer's Knives, Beam of the Inferno, etc.).