That's the thing though; I shouldn't have to sacrifice mage freedom so that the antagonist is more interesting. The same amount of content should be available for both alliances. I'm not shocked though -this just another example of Biowares incompetence.
Personally I think the story is far, far better with the mage path (though I think champions of then just is the better mission standing alone). The Elder One is an existential threat on that path. You see the culmination of his plan at Redcliffe in the dark future, and the bleakness and devastation he visits on the word. You also see the horror brought on by the red lyrium. When Corypheus appears with a legion of monstrous templars, you see the reflection of dark fate awaiting all of Thedas if you fail. When he crushes the Inquisition at Haven, it adds to the hopelessness of the situation - not only did he break you, but perhaps his dark victory in the future is unavoidable. It makes the Inquisition's need to believe that the Herald was sent by the Maker all the more important to them.
I dunno, after playing through the templar side of things, I don't think the temple of Dumat in any way makes up for all the bleakness that gets added by siding with the mages.