GURPS is fine in a realistic game. All the realistic advantages are fairly priced, no need to apply any modification. I cannot say the same in a game with Supernatural advantages. Here is where best practices and GM's world building are going to mean a lot of work.
Recently I discovered the cheese of Modular Abilities (B71) with -80% limitation (B110) (example - Preparation Required 1 hour -50%, Limited Use x10, -10%; Spells only -20%) (any combination of limitations). Its quite powerful, but before that I've struggled with powers reflecting the setting demographics - how often they occur and how the market prices such magical modification.
An interesting way to do this is creating a set of Tiers. Each tier is a Multiplier to the Cost of an Advantage or Power. Tiers multiply the cost, x1.5, x2, x3, x5. You can do this Before the Campaign begins or tweak it around mid-campaign. Of course, your players should be aware of this if its mid game. Of course you have to go to the forums and check what needs to be "tweaked" and what creates interesting organic results. Personally there should be some list of powers that can be calibrated. Modular Ability + Magic is one of those. Some people argue Magery IF you allow them in certain levels.
Why Doctrine - More Organization of Material, instead of More Material
The added cost only makes certain powers occur more often than others, and what happens next is Doctrine. This is what I wanted from my WBH game. See how best practice evolved from the game system, and I discovered some interesting combos and practices as a result of certain advantages and combinations. My regret is that magery is just TOOO big a chunk to process, especially when you consider the number of books about it. We've reached the point of diminishing returns, that we need more Prepared Material, like Doctrine, instead of New material. An aging number of players, the highest paying bracket, won't be very easy to part with money if its something that just adds work instead of reduces it.
I like doctrine, its something the GM can be good at even if hes not as smart as a bunch of players combined or those who can dedicate their resources and time to their character. With doctrine you have guidelines and procedure, it draws upon more of age and experience instead of brilliance and processing ability. You can pulls something out chaos and it will screw with a lot of things. It empowers the GM to give a real challenge.