In regards to having a mage as an advisor - while I do like the idea, I think the three pillars of the Inquisition do make sense as they are, and I'm going to echo other posters in this thread and say that I believe Morrigan will be our unofficial consultant for all things magic-related, as far as non-companions go. Also, it is possible Dagna will be around, so maybe she can advise us in a scholastic capacity. And, we have three mages as companions - each with their area of expertise. And personally, I think they do us a lot more good on the field - where they can actually see the things we're dealing with and actually physically aid us.
And, to those of you disappointed in the pro-Chantry/Andrastian slant of the Inquisition's leaders - well, the Inquisition itself is an organization conceptualized and put together by the Chantry. For those players who are pro-mage/anti-Chantry, and wish to play characters that are as well, well - yes, the Chantry-loyalists lead the organization, but - YOU are the one with the power. And YOU are the one in control. No, you can't dismiss your advisors, but remember they serve you. And what better way to subvert the Chantry and all its ideals than to have a non-Andrastian be the one to save the world, making it clear all the while that they do not believe their so-called 'gift' had anything to do with the Maker? Bonus points if you play a mage, in my opinion.
Edit: changed 'Chantry-lovers' to 'loyalists' - probably a more accurate term. based on what we know