I'm not so certain that the question should be 'whom do you trust more', rather than which one has the World's best intentions in mind.
If you're really asking whom to trust, I think it's on a personal level. If you want to know which of the two have the best intentions to save the world, that may be more a matter of experience and knowledge of the past, and what is currently happening in Thedas.
Let's face it, neither Morrigan, nor Flemeth, are out to destroy the world. Neither seem to have an agenda regarding ultimate power. Flemeth didn't really seem worried which way the Warden decided (kill her, or lie to Morrigan) in DA:O, and it turned out she was already prepared for either outcome (hence the amulet for the Dalish in DA:2). She also gave the Warden help in the way of Morrigan to defeat the Archdemon because she knew the consequences of the blight on the world.
Morrigan distrusted Flemeth because of what she found in her Grimoire regarding hints that Flemeth used her 'daughters' to extend her own life. Morrigan was also as 'in the dark' about Flemeth as the Warden and everyone else was, despite having been raised by her. Secrecy does not necessarily mean evil. And tall tales aren't always factual. Not that Flemeth had no problem handing over her second Grimoire (found in the Circle, no less) to appease Morrigan.
In my own opinion, both have the same goal of saving the world from the blight. It's the Warden's trust, or mistrust, of each that wholly depends of information, or lack thereof. Whether or not Morrigan was romanced shouldn't really matter because it creates a biased opinion. Flemeth, isn't going to tell everyone about what she sees as future potential because that knowledge could possibly create problems if people respond in the wrong way (if the Warden were told they were expected to die without a chance of saving themselves, would anyone actually join?).
To me, Flemeth seems to have a better understanding of the future, and the consequences of actions, while Morrigan seems to be almost as much in the dark as the rest of us, but she's afraid that Flemeth has plans for her, or her body, that she doesn't yet know about.
Would I trust my life to either of them? Yes. In a heartbeat. They've both proven that we three share the same goal of defeating the blight and saving the world.
Do I believe that either of them have my best interests in mind once the danger has passed? Absolutely not.
But, if your goal is to be rid of the Archdemon, the Darkspawn, and reach toward a better Thedas, I'll place my trust in both, and cross my fingers that it was the right decision.