... It looks to me like you're using two different measuring sticks here for Templars and mages, or am I reading you wrong? For me this reads like: Templars (probably) had doubts but didn't act on them fast enough = not their fault vs Fiona (probably) had doubts but didn't act on them fast enough = her fault? At the very least, Fiona was a victim of betrayal (Venatori in the ranks) and circumstance (Templars at the gates) at least as much as the Templars.
Also, when demon-Lucius comes to VR, he tells the people there the Templars "failed no-one then they left the Chantry to purge the mages" (yes, that ad verbatim what he says - and let's not beat around the bush here: he's talking about genocide) after one of his mooks punches a priest in the face while he doesn't bat an eyelash - and even after this Templars (including Barris) follow him to Therinfal Redoubt. That kinda balances the scale quite heavily in favour of the mages for me. Not saying there are not decent people kicking around in the Templar order - or that they wouldn't have eventually come to their senses - but if I have to choose between these two groups, I'd rather choose the group whose leader made a bad decision out of desperate need to save her people over a group who didn't leave although they absolutely could have (and possibly were offered an option to leave, if you choose the "Templars! Join as Cullen did!" -dialogue option) without any immediate repercussions (although the lyrium withdrawal is a pretty major thing - ugh, Chantry sucks) - mages never really had that option without risking either their freedom and/or their lives.
Also, story-wise I think IHW is more urgent IMO - Redcliffe is closer to the Inquisition's base of operations than Therinfal is, and having Redcliffe fall under enemy control is Very Not Good (as Leliana points out) - not to mention the whole time magic thing. In contrast, we have "something weird is going on in that way direction - maybe" doesn't feel so urgent / time-critical to me at that point in the game. And when it comes to gameplay differences, different strokes for different folks. I am in general not a big fan of Fade (although I really liked the Fade-portion of Here Lies the Abyss) so CotJ doesn't exactly endear itself to me, although I really liked the first introduction with the advisers. But the rest of it... just not something I enjoy, particularly since I have to trudge through most of it all in my lonesome. Plus, I thought that even though I usually loathe time travel storylines, having the Envy demon outright show you its plans in the Fade felt even more ridiculous. It's like the ultimate Villainous Plan Reveal Monologue - at least in IHW people know about Cory's plans because that's what happened. But again, I guess that's a matter of taste which not-all-that-great plot devices you like most / dislike least.
Not different measuring sticks, just judging them based on their different circumstances. Fiona had no obligation to Tevinter, and she knew she was getting into a bad situation. "Evil" Tevinter, 10 years of slavery for the promise of full citizenship afterward. This was after Alexius transgressed against Teagan and angered Ferelden. The templars on the other hand were sworn to follow their leaders. And like I said, they were corrupted from the top down. But Fiona was the top of her group. The alternative to Lucius for the templars was an organization that was branded heretical by the Chantry. And the templars needed notoriety. The alternative for the mages was an organization that had already taken in mages and was established separate from the Chantry. And the mages needed safe haven. Ha, haven. Get it? The sales pitch writes itself. So Fiona had every reason to go with the Inquisition and ditch Tevinter. The templars still needed reasons to go with the Inquisition and ditch Lucius and the other commanders.
Lucius is talking about genocide against an army of mages that were blamed for blowing up the Kirkwall Chantry, rebelling against the order of the Circles to have free reign of the countryside, and I think the conclave was blamed on them as well. Some of those mages were also hostile, even if the main group of the rebellion distanced themselves from them.
The donkey punch to the poor old Chantry mother was harsh, and Barris was disturbed by it, but Lucius talked his way out of it by talking up the templar order. It's also possible he spun this to say that it was a templar (who I swear is Denam based on the voice) who decided to punch the mother, but Lucius stood by the action of the templar because he supports his fellows just that much. But even after reaching Therinfal, Barris confirms that the templars thought that was a shameful display, that they had been asked to accept much since then, and that many templars questioned why they were there when the Breach was the obvious threat. I suspect Lucius convinced them that the world would turn to the templars as their saviors once the threat of the Breach became to much to ignore. At that point they would be able to demand recognition, independence, and respect for all the sacrifices templars have to make in order to keep the world safe. But by the time they came to their senses, it was too late. Too many would have been corrupted by the red lyrium.
The mages' freedom was already risked when Fiona made the 10 year slavery deal.
Leliana does point that out, but Josephine also points out that Arl Teagan had gone to Denerim to get military support from the crown. Which means the problem in Redcliffe would have resolved itself. There are many pros to getting the templars, and many cons to going after the mages, which I won't go through now, but I think templars are the best option in all cases except for very specific circumstances, all of which are based on what kind of character you play.
Time magic might seem like the more pressing matter on its face, but if you examine the illogic of confronting it head-on, I think it will prove that CotJ is the best course of action in... again, all cases except those of specific circumstance. Theoretically, if Alexius controls time itself, then there is nothing you can do to stop him. Any attempt you make will just be countered by time magic. Which means Alexius already knows what you are going to do to stop him (he knows you know its a trap and have snuck scouts into the castle with Dorian's help), but from your perspective you haven't tried it yet. Thus the best course of action is to avoid the trap entirely and let Ferelden's crown risk its soldiers against the time wizard. In the meantime, you fortify your own defenses to be on the lookout for Alexius, since he might try to attack you while you go to Therinfal. Having an impenetrable defense is all you can do in that case. Alexius can try to attack you, fail, and then have maybe one more shot at attacking you again if he goes back in time. Though chances are he would rather take that time to avoid a killing blow from Ferelden's crown and escape with all the mages to the north (which is exactly what he ends up doing).
As for the envy demon vs. the bad future, I think the envy demon's approach is the better storyline device actually. Well, halfway anyhow. It is cool to learn about the demon army and Celene's assassination from the bad future. However, there are quite a few things you should learn about from the bad future as well, such as the Elder One's name, or the fact he has a dragon that many think is an archdemon, or that the templars at Therinfal will be turned into red templars, or that Haven will be attacked. Varric should have been able to recognize Corypheus on sight. Solas also should have been able to tell you, looking at this in retrospect. But none of that is revealed to you, when logically it should have been.
With the envy demon, I think it was awesome to have the plan of taking your face and commanding a demon army shown to you in order to gauge your reactions to it so the demon can better copy you. It was a mix of feelings for me. On the one hand it was a startling and horrifying scheme, yet I also didn't want to give the demon any reactions to copy. And this makes sense because Envy thought it had you and that there was no way you would be able to break free from it. Plus, Envy wasn't all that smart. Now, the part where you just walk into a room with a murder knife embedded in a bust of Celene? That was kind of lame, but I see why BioWare had to do it that way.