I wouldn't say the red templars are better enemies so much as I think they make for a better tone. With what you see in the bad future - a world overrun by red lyrium - it makes Corypheus seem more threatening (because it looks like he will absolutely win if you don't interfere). Whereas with Therinfall his mooks aren't terrifying (they're just mages) and you don't really come back to Haven harrowed by the experience in the same way.
My view is that hushed whispers really sells the stake of the threat- but it's CotJ that carries the tone better after the Breach is closed.
Hushed Whispers has a really strong intro, don't get me wrong- it's got a compelling hook about why it's important, even more important, than the Templars. And time magic definitely sells the importance of closing the breach- how the world is breaking apart, demons everywhere, and people we know (and maybe even like) will suffer for it.
But after the Breach is closed... the mages are pretty meh, all things considered. Fiona isn't a participant, or a significant contributer, and the mages don't really distinguish themselves: most of their war table missions involve bringing in strays and mages who went to ground, which is nice and all but really doesn't have much on stopping demonic attacks on major cities.
In addition, the Red Templars are... well, it's a case of DAI getting confused about what sort of enemy we're facing. Is Corypheus an army, or a conspiracy? Red Templars are the former, but Corypheus's plot as a whole is the later- and, yeah, I like Empress De Lions as much as the next person for a sense of a major battle against Corypheus, but that's about it. Thematically, the Red Templars are a wash: they're the worst sort of brainwashed foes, who have no ideology or rational for their actions because they're just mind-controlled slaves. Sampson has a pretty weak character arc about how they're fighting the Chantry that used and disregarded them- but he's one-off, poorly supported, and his reason for following Corypheus amounts to spit. His subordinates don't share his feelings on account of being, well, mind-controlled slaves. It's even worse than Cerberus in ME3: Cerberus could claim it was going for a long-shot gambit of Human dominance, but the Red Templars have nothing in common with the actual Templars other than armor. There's no anti-magic/anti-mage vendetta, not even a real idea of if the Red Templars are capable of anti-magic, and they're serving mage supremacists because... well, no reason than addiction and enslavement.
It's a weak antagonist (Samson), and a underwhelming ally (Fiona) for Hushed Whispers.
On the other hand, Champions of the just really picks up with the merits of actually recruiting the group. Unlike the mages, who are passive to their own recruitment and within their own mission, the Templars are enthusiastic- they fight with you, they'll fight for you, and they directly admit to their own failings in a way Fiona refuses to. Almost immediately they are a credible boon to the Inquisition- manpower when we're still strong, public support, and their own support networks that the mages do not have. We're told regardless that the Templars the Inquisition has gathered up are the core of our forces, and damn if it doesn't make more sense whether you ally or conscript them. Plus, in their war table missions they go out and do the things the Inquisition stands for- restoring order, fighting demons, managing the fearful masses in the pursuit of truth. Baras the Badass becoming the head of the Templars is a high-point for later in the game, an excellent goalpost for the Inquisition's rising strength- and one with no Mage equivalent.
No only is the quality of your ally better, but the quality of your rival antagonist is improved. Calpernia and a cult of mage supremacists makes sense as an ally and tool for Corypheus. The Venatori not only have the ideological/thematic parallels with Corypheus- mage supremacists, Tevinter- but they operate like Corypheus as well- conspiratorial, secretive. Calpernia is a much better rival to Leliana than Samson is to Cullen, and the Inquisition-Venatori matchup is much better in terms if the premise of the Inqusition- to inquire, to investigate, to ferret out- than the conventional battle force that was the Red Templars. Our allies work better for it as well: we have Templars, trained and experienced in hunting maleficar, and our primary enemies are maleficar. Whereas in Husted Whispers, we take a mage force that was soundly beaten by the Templars, and... well, we don't really make exceptional use of them against the Red Templars.
Calpernia and Venatori? Better enemies. Evil- but thinking evil.
Or so my thoughts go.