My last word and opinion on the actual question which is better between Champions of the Just or In Hushed Whispers, since this current conversation is just a retread of Mage vs. Templar like every other thread.
1. Companion introduction: In Hushed Whispers > Champions of the Just
You get Cole during Champions of the Just and Dorian during In Hushed Whispers, and whomever you don't get is introduced during the attack on Haven. I liked both mission introductions, but Dorian wins out for me for being playable during In Hushed Whispers. I also preferr how Cole is introduced in Haven to how Dorian is if you went with the Templars first.
2. Plots: In Hushed Whispers > Champions of the Just
I'm not making a call on which is better, I was just more interested in seeing the Bad Future were The Elder One wins as opposed to a Battle in the Center of the Mind with the Envy Demon. That, and I feel it more urgent to liberate Redcliffe from Tevinter rule instead of going off in in the middle of nowhere to investigate some Templar compound.
3. NPCs: In Hushed Whispers = Champions of the Just
Ser Barras is probably the most badass Templar in the franchise, while the Envy demon is really creepy. I like Fiona, though I'm not blind to why other hate her, so it was nice to meet her finally, Nice to see Connor again too. Alexiuis and his son are tragic to me, but I can enjoy doing whatever punishment I please to Alexius afterwards.
4. Music: In Hushed Whispers < Champions of the Just
Just had better battle music to me.
5. Boss fights: In Hushed Whispers = Champions of the Just
The Envy Demon and Alexius are the same mechanically. Soak up damage, run and summon minions to beat up party, rinse and repeat.