i'm not too good at expressing my opinions, i can't quite put into words why the story and characters stick out to me more than the other GBA games, but they do.
gameplay-wise, though... to me it actually feels like it was trying to do something. sure it wasn't perfect, and it didn't exactly do anything new, but it did more than the previous two.
Binding Blade and Fire Emblem felt too bland to me. they just have the most basic design in the series - they do pretty much nothing that most of the other games don't, but Sacred Stones brings back the world map, branching promotions, and skills (even if they were so limited), and it has its split story paths - it feels like they tried more than with the previous two, and i like that.
but then again i specialize in the first 5 games so i may be missing some things from 6 and 7. honestly they just don't interest me as much as Sacred Stones. it's far from perfect but just barely does things right enough to keep my attention. (disclaimer: my idea of "right" is heavily influenced by my opinions on shouzou kaga so if you're sick of hearing about him then forget everything i said)