I love Sacred Stones for a few reasons.
I actually very much dislike Ephraim and Eirika, yet this game is still my favorite GBA Fire Emblem. Ephraim seems too much of an overpowered guy, and Eirika is just kind of dumb/useless a lot of times. Which is a shame, because the storyline in this game was good.
My first reason is the villain of the game. Lyon is probably my favorite FE Villain (sorry Black Knight). He has actual personality, and was a great friend to the main characters, making you able to see actual emotion from the Lords. It's no longer just a "Let's save the world" situation, it's a "Let's get revenge for our friend."
I also love the idea of Trainee units, which I wish they had brought back for FE14 (NO MOZU IS NOT A TRAINEE UNIT). The idea of getting to promote twice and get even more of a choice on how a unit turns out is an interesting concept, although I can understand why they didn't include them, since Heart Seals and such are a thing now.
FE8 also felt like it heavily influenced later games, such as the world map, encounters, and different routes.