Avalon Code is good and has a great plot line and it's a pretty long game. The dungeons can get a little tedious sometimes (because they're challenges like defeat all enemies), but that's nothing big and is usually only once you've played it several times. It does have a romance aspect to it, but you don't have to follow through with that if you don't want to. The graphics are great for a DS and the fighting's good. The plot line is out of this world, it makes up for any of its shortcomings.
Dragon Quest is usually good and has good plot lines and is quite long. It's kinds like Dragon Warrior and has a turn-based combat system.
Ateller Annie is pretty good. There are some characters that are in other games of the series, but it's plot line of its own. It has a turn-based combat system.
Pokemon, like you said, is the best :3
Final Fantasy is good. It's a long game, but it has a pretty good plot line. It has turn-based combat, and you don't need to know anything about the other Final Fantasys (I know because I don't know anything about other Final Fantasys)
I know that you said no romancey games, but Rune Factory is awesome, and unlike the ones you listed above. In this you actually fight monsters. In the first one there are a ton of caves and romance isn't neccessary. In the second and thrid it is, which sucks, but it's the only way to progress the game. For the second one I was stuck for months before I looked online and realized that you had to get married to progress the game. Other than that it's great!
Spyro is good, better on PS, but good nonetheless.