They are both popular. In Japan, FE6 is considered one of the best.
They both saved the franchise though.
FE6 was the first game in years. It was the revival of the series.
Yeah, I do believe FE6 is high up in terms of GBA game sales in Japan (my sources are saved on another computer. Gonna see if I could accesses them later).
And it was a while until FE6. There was a planned FE game for the 64DD, but got cancelled. And I don't think we know how far it was into development, if it got any development at all. Not only that, but the creator and developer of FE, Shouzou Kaga, left after Thracia 776. The FE5 --> FE6 transition was pretty big and I do think we're seeing something similar with Awakening in terms of the games being more accessible and the audience being widened.
I do hope that FE6 will get a remake if Roy returns, though. Thanks to Melee he has some exposure in the West, and higher-ups at IS did express interest in a remake. We'll see I guess, I don't want to keep my expectations high when it comes to these things.