There might be minor factions we can "hopefully" add to our Inquisition forces
I hope that this is the case as well.
I also hope that some of these other "minor" factions include the fantasy elements of the DA setting. I would love to be able to recruit the various supernatural entities around Thedas to my Inquisition to bolster my 'normal' forces; and not just because I like the 'alien' parts of the setting more then the human conflicts, but also because these creatures would offer aid in a way that no Human, Elf, Dwarf, or Qunari could.
I know that I would much rather have a handful of Golems guarding my keeps then a whole battalion of human warriors; chiefly because Golems don't need to eat, or sleep, they have immense (rock crushing) strength, they can take a heck of lot more punishment before falling, and they don't question orders. Likewise, even the most attuned Dalish hunters pale in comparison to the raw, beastial instincts of a Werewolf; not to mention that the natural weapons and armor of the were creatures means that I don't have to supply them with arms like I would for my regular forces.
I do hope that such alliances are not the psychotic, evil choices though. I don't want to have to burn a village to the ground and then impale all the children on spikes just to enlist the help of the Sylvans for my army, for example. Something that doesn't have a direct human analogue, or isn't immediately identifiable with human preconceptions, or cultures ≠ Evil Monster and I hope that such factions are presented with more depth then that.
I am going to have to disagree with the OP and say that I don't want all choices regarding the factions of DA:I to be binary in nature, I would like to see compromise in the list of options as well. Instead of having to pick only the mages, or only the templars, I would much rather have the ability of working towards or forcing an agreement between both factions. Obviously, I wouldn't want the middle ground choices to reward more allies then picking one faction over the other; in fact I would submit that such a compromise would net players with a smaller boost to their forces then if they just helped the templars or the mages. Maybe in order to get both sides to agree to work together you would have to eliminate the hardliners from both faction's leadership, the act of doing this however will negate any bonuses that you might have got for keeping said leaders in power.