Doesn't Flemeth say when she meets Morrigan and the Inquisitor that she wants to get revenge for Mythal's betrayal and murder, and that "it shall be a reckoning that shakes the heavens"?
Since we've learned in Trespasser that the "Elvhen Gods" betrayed her, they might be the ones she wants vengeance on. Since Solas made the Veil that formed the heavens in the first place, and imprisoned them there as punishment for killing her, I get the impression that she wants to amass power so she can also either break down or break through the Veil to kill them.
"But why collect so much power, and the souls of Old Gods?" you might ask. When Solas reveals that he wants to tear down the Veil, Lavellan can ask, "But what about the false gods? Won't destroying the Veil free them?" and he'll say "I have a plan."
It's possible that even though they've been imprisoned for centuries, they're still powerful and can wreak great havoc once unleashed. Flemeth said that Mythal was "but a wisp" of what she once was, and had been "crawling and clawing her way through the centuries," and implies that they've been amassing power ever since. It's possible that she's been collecting lots of power so she'll have the power to kill them once she reaches them.
It seems that Solas' and Mythal's plans are similar, but their priorities are different. I'm guessing Mythal wants to break through or break down the Veil to kill the elven "gods" for killing her, but doesn't seem too concerned with the fate of the elven people. (If her reaction to the Dalish Inquisitor is any indication.) Meanwhile, Solas wants to tear down the Veil to restore the elven people, with the execution (or however he intends to deal with them) of the newly released gods an added side benefit. Since what he wants to do likely involves what she wants to do, I think that's why she's going along with it.
That, or Mythal has another trick up her sleeve that Solas doesn't know about. I wouldn't put it past her.