Advance Wars DS The other Advance Wars games are great too, I didn't like Days of Ruin as much due to the grungy art and the fact that it didn't have previous games' characters in it, but the writing was still really good. The writing for AW is brilliant; it's funny and insightful and I just love it, the characters are so deep; few games manage that. I really hope that they use the original cast of characters for the next one. The Fire Emblem games have good writing and characterisation too, FE is made by the same developer (Intelligent Systems). Majora's Mask (Although the three day thing can be pretty annoying, it making it possible for NPCs' lives to be so detailed and focus so strongly on their personalities more than made up for the frustration IMO). Just two of many.
Dungeon Maker/master of Monster Liar (is the same game but it has two different name...) Yggdra Union Knights in The Nightmare and some other Atlus RPG
Try Final Fantasy 4 Final Fantasy ( Not a good storyline but cool Gameplay) Sands Of Destruction Shin Megami Tensei Strange Journey and Devil Survivior
Soma Bringer classic rts-rpg(Diablo for pc comes into mind) good story there is a translation at gbatemp if your interested
Also try Suikoden Tierkreis Ragnarok DS (Storyline isn't good but the gameplay is cool) Final Fantasy Crystal Chronicles Rings Of Fate (Better Story)/ Echoes of Time (Better Gameplay)