If your PC does not go to the chantry after speaking with Alexius, then there is no reason to think that Redcliff is more urgent. You receive a note saying "go to the chantry, you´re in danger", so this may as well be a trap - like some companions point out. If you go you meet Dorian and learn all the stuff, but if you don´t go then you simply leave the mages with their shenanigans and go recruit the templars instead.
This is what i do in my canon playthrough in order to avoid the time-travel plot, it is never brought up in the game if you don´t go to the chantry in redcliff.
This is actually a very strong and reasonable point- enough so that I almost wish that the war mission either-or choice had been placed here, rather than after the reveal of time magic. Rather than a note of 'meet me at the chantry' that you could walk to, something that also required a war mission to investigate.
Because, let's face it... the reveal of time magic makes Redcliffe really pressing in differing ways. And yet- the nature of the note delivery itself could have been played up for suspicion and tension. Playing it as 'this is such an obvious trap, let's take our leave and GTFO for some Templars' is a strong argument.
That all said, moving back to the main topic...
While I find some flaws with the two choices on their own grounds, I actually highly enjoyed and appreciated the difference between Champions of the Just and In Hushed Whispers. Despite the things they did wrong (a weaker time-travel story vis-a-vis a less developed lead-in), what they did right was numerous, and offered a variety of legitimate and reasonable ways to rationalize either choice.
That meant a lot to me, so I'll say it again: I really, really like how they made both choices justifiable on multiple grounds. Mages vs. Templars was successfully split from one's view on the Mage-Templar conflict, to the point that while one's politics could influence a choice, it was quite possible to rationalize a good reason for choosing your disliked size. Templar supporters could be concerned enough about the Mages to trust the Templars to hold themselves together while fixing Redcliffe. Mage supporters could find Fiona so out of control that bringing in anti-magic support would be sound thinking.
I like that, and I don't even have a 'preferred' choice on a overarching level. It's always RP dependent- and I never feel like I'm breaking character to choose the one I want to.
That said, on a personal level... I think Inquisition as a whole does a better job leading into the mage story, but does a better job carrying the Templar story.
The mage lead-in has numerous advantages and appeals: it consistently casts the mages sympathetically from the start with the antagonistic Templar woman-beaters and Fiona's diplomatic appeal as the contrast. There's a more developed sense of accomplishment in reaching them, since you fight your way to Redcliffe and explore/overhear the context surrounding them. The flaws of the arrangement are better developed- not just overtly, when we find evidence and hear of Fiona's incompetence even as we sympathize with the mages for abolitionist sentiment against the obvious villains, but also in the ambient encounters (the mages with varying degrees of acceptence/support for the Tevinter alliance) and in the subtle/unspoken things that are found rather than presented. Finding the tranquil skulls, overhearing about the expulsions, putting the pieces together- and then the Time Magic reveal with the meeting with Dorian. All together, a very strong intro and lead-in to Redcliffe: we know what we're going into, we know why we care, and their are faces and names to consider.
By contrast, the Templars have a weak entry since it's almost all War Table. Yeah, we get a token Templar rep who talks about how they aren't all bad, but mostly our advocates are advisors. Our reasons to not want to, however, are the openly and uniformly antagonistic encounter we have with the Templars in Orlais- including the shocking cultural taboo of hitting a woman. Le gasp! After which... well, Cassandra raises a red flag about how unusual it was, but we have to take her word for it. And ignore all of the above. Even though there's good reasons to do the Templars, they aren't as obvious, or raised as much, or supported with content.
So leading up to the choice, I'd say Hused Whispers is stronger.
After the point of no return, though...
I think that, roughly, the missions themselves are equally good in different ways, and that they both support the story.
Hushed Whispers is, in my view, far better at establishing Corypheus as a real threat. Time magic allows us to see and know that the Elder One has won. The tension, the fear from our companions, the dramatic race against time as He approaches- it's dramatic and tense and appropriately apocalyptic, vis-a-vis Envy's 'let's show you a delusion that you never have to accept the validity of'. When we get back from the future, we can really believe the world is ending... and then we have the corrupted Templars who can do it. We beat back Corypheus after seeing he can and will win if we're not successful, even as he beats us at Haven shortly after. Hushed Whispers sets the stakes.
Champions of the Just, however, works better on the thematic level and in treating the faction of interest as, well, nuanced. In Hushed Whispers, the mages were non-entities: they were practically irrelevant, represented only by Fiona, with no dissent and no real role in deciding their own fate. Whereas the Templars in COTJ are just as involved as the player is in preventing the catastrophe. The Templars are torn and divided amongst themselves. We see the evidence, and the fighters, bravely fighting against what is wrong, enduring the betrayal of their superiors and rooting out the evil amongst themselves. We not only see the best of them- we see the worst of them, and judge them accordingly. It's a shared victory, and the Templars grateful allies and penitant for their failures, and whether we ally or conscript them there is no question that the Inquisition comes away far better for it. Unlike Hushed Whispers, where the Mages are a prize who don't even determine their own fate, Champions of the Just is a battle in which we truly earn worthy allies- and plays into the Inquisition's character themes about uncovering and addressing deceits and hidden evils. We never do that to the Mages, but it's worth noting how we can do that to our Templar captive for judgement.
After the recruitment...
I prefer the Templars, full stop, for the fulfilling the role they play.
The mages are never that credible a boon to me. They're few. We're told from the start that they're mostly noncombatants. It's rarely clear how the Inquisition benefits from the mages more than the other way around... and you know what, that's mostly fine. But as far as the 'rising power, beloved by the people' idea goes, the mages are an albatross, not an answer for that. The mage results we see later are largely less than impressive: Fiona stands around waiting for the Inquistior to do everything rather than provide meaningful help (which, sadly, is probably the best decision she makes), various mages complain about their circumstances afterwards, and while some mages step out of hiding to volunteer to help, there's little of note achieved and no clear reason why they couldn't/shouldn't do the same regardless.
Whereas the Templars are a credible asset from the start. Here are numbers and skill dedicated to your cause that makes sense to jump the Inquisition to 'minor force' to 'modest power.' Here are experienced mage hunters, maleficar trackers, and respected guardians of the people who not only are better suited to track down the Tevinter maleficar we call foes, but benefit and win the respect of the common people doing it. And they do do things: Ser Barris the Badass puts Fiona to shame, the signficant numbers of men credibly patrols and hunts for demons, and they compose themselves admirably in their professionalism despite the tensions between them and the Inquisition's mages.
There's also the nature of the foes. The Venatori are, to this day, a mostly free-willed group of mage-supremacists. Not all Circle mages in Redclliffe joined them, but a key point of their 'recruitment' to Corypheus was that they didn't need to be brainwashed- they made one bad decision after another to get to that point. Whereas Champions of the Just makes very clear that the Templars had to be tricked, betrayed, and ultimately brainwashed to become the villainous Red Templars: that their trusted leaders had to corruptly poison them, addict them, and enslave them, and that if they had the chance (with the Inquisitor's help) these Templars would have fought back.
That's a degree of moral 'worthiness' on 'who deserves to be rescued'- but it also plays into the wider themes of Inquisition about secrets, free will, and compulsion. Corypheus's real danger isn't him brainwashing everyone into slaves- it's how many people will agree with him for their own reasons by their own will. Which also ties into the quality of rival for Coryphus's Dragon.
Calpernia is a zealot leading supremacists- whereas Samson is caretaker of a bunch of addicts and slaves. Fiona sold herself into slavery, and wouldn't rise against Alexius even as he blatantly changed the terms of his deal- whereas Barriss has his doubts from the start, and will give his life to defy the Red Templars. Considering that Inquisition doesn't play well or consistently with how much of a threat Corypheus poses with an army, I prefer the Venatori as the primary antagonist. The cult plays better in the Inquisition's theme of uncovering the truth and ferreting out corruption, and is a more consistent play in the Corypheus 'let's use mega-magic to conquer the mundanes of Southern Thedas,' whereas the Red Templars... well, the 'production' of them had a point, but they were never the real threat. Corypheus's army of demons is what would have conquered Thedas, while the Red Templars were never a threat to either nation of Ferelden or Orlais. They were useful, but not dangerous as the Venatori.
Overall, in the mid/late game, I feel the Templars simply do a better job being a support group for the Inquisition's development than Fiona's mages do. The allied faction is better, the enemy faction appeals to me more, and I think there's stronger thematic integrity across the arcs.
But that's just me and my rambling.