After playing both, I also must agree that the Templar playthrough seems to be the most fulfilling. All the previous people covered why excellently.
One other point: I'm a very pro-Mage person. However even I was beyond disgusted with their siding with Tevinter; and couldn't bring myself to ally with a group so diametrically opposed to what's in its own survival interests. I assumed Fiona was being controlled through blood magic, and indeed that seems like a dropped plotline, but no; she's just an idiot. So in my first playthrough I conscripted their "too-stupid-to-live-free" asses. A no-win situation either way, in my opinion. Gain idiotic, backstabbing allies, or gain a slave army.
A couple of people have suggested you also get this option with the Templars. You do not. You either pledge to help them rebuild their order; or, and your Inquisitor painstakingly uses the phrase "our offer" several times, disband them and have them freely join the inquisition as one of its military arms. Either way you get willing troops. Much better in terms of what strengthens the Inquisition.
So many people feel the Templar side was better. Now just imagine if they went with the original plan; with the fake-end to the Act and such. The Mage side wouldn't even stand a chance.