Overall I think I do prefer the Templar quest because playing through it is more interesting but at the same time I may still end up choosing the Mage Quest seven times out of ten. Mostly because I prefer to play elves and, unless Josephine is a miracle worker, I have a hard time believing that ten Orlesian noble families would rally around an upstart Dalish Elf.
Other than that, it's just the fact that it's a Tevinter Magister involved in what's going on at Redcliffe. Time magic and a hostile foreign power right within Fereldan's borders and in one of its more important towns always feels a bit more urgent to me. I mean, I know it's just the Venatori and not a chunk of Tevinter's army sitting in Redcliffe but it still doesn't seem like something you should just leave alone.
My train of thought is that by chasing the Templars you aren't just flat out abandoning the situation at Redcliffe, if you ask where Teagan is in the Mage briefing, they say he rode straight to the capital to get the monarchs aid and likely wouldn't need you when they have besieged the place.
So the situation is likely to be handled if you do nothing, where as the Templar would still be unaccounted for, so may as well handle the faction that doesn't have a solution in progress. Add in the fact that the Mages voluntarily deferred to Fiona who sought to find refuge in Tevinter, their choice was made, hardly seemed my place to bail them out of a bad deal. All that combined with weakening the breach seems wiser than powering up the mark makes it hard for me to side with the Mages.
Though I do enjoy how character defining In Hushed Whispers can be, previous lax and sarcastic character all of a sudden is given massive motivation to aim up, get serious and succeed at any cost.