The biggest limitation on the magic system is that most people can't do anything major. There are many people with the potential to use the Nine Disciplines (to be one of these people, you need to have a certain blood type) and if you can use one, you can use all of them. Some people have a greater affinity for one particular Discipline, but they always have the potential to use them all.
The problem with the Nine Disciplines is the fact that it takes a good amount of talent or training to be able to do much with them. There are plenty of people in the world who can use the Disciplines, but they only use them lightly, and never get any better with them. E.g. A person who has an affinity for the Physical Discipline uses it every once in a while, but can only make themselves a bit stronger or faster--not enough to make them "magic-users" as the term would be in a D&D setting.
In essence, the Nine Disciplines are mostly used as another "skill set" along with knowing how to use a sword, or being able to play a lute. There are definitely exceptions to this--people who are either naturally more skilled with magic or spend a lot of time training with it--and they are considered the clerics, wizards, and druids (per se) of the world.
(Now that I think about it, maybe I should come up with a specific reason why some people are better with it and others aren't... I'll have to think about it...)
Also, using the Nine Disciplines in any way tires a person--and they get tired slower or faster depending on how skilled they are and how much they've trained with them.
It CAN get pretty powerful, but no where near to the extent of some D&D settings (Forgotten Realms springs to mind). These individuals are few and far between, however, and so it's not quite so dangerous as one might think, just reading the description of what the disciplines can do. Most of the examples I put in there are actually sort of on the extreme end of the spectrum--some of the more potent things you could do.
How much you can use magic sort of depends on what power source you are using. For example, clerics are limited to "spells" that would line up with their deity's personality and values--not really a "forbidden" thing, but rather an "impossible" thing. A cleric of the god of peace just CAN'T kill someone outright with any sort of magic, their god won't give them the energy to do that. Wizards are limited to the spells they know/have with them, since their power comes from specific words, phrases, or incantations. And so on and so forth...
The only thing I can think of to shield mind manipulation is having access to the Nine Disciplines yourself (or having a friend who does). But most of the time the people who can use it are few and far between, so there's not a general problem of people messing with your mind.
One of the things about magic-users is that you HAVE to have a power source. You could go your whole life and never know you have the ability to use magic, simply because you don't have a power source. That's why most magic-users are in specific groups--because only those groups have access to the power source and can give the knowledge of that source to other potential magic-users.
And about the Essential Discipline--once again, the majority of the time, there just aren't that many people around who can bring people back to the dead, mostly because it's stinkin' hard to accomplish.
I am definitely thinking a bit more about this, and I'm going to go through each of the Disciplines and specifically state things that are more or less impossible or almost impossible to do with each group of magic.
But yeah--thanks for your input!
Oh, and yeah... I guess you're not creating new energy or matter... more like using the magical energy to create something.