I prefer the Final Fantasy series because it isn't scared to innovate. Final Fantasy almost always had the upper hand when compared to Dragon Quest, from the music to the battle system to the story and character development. Dragon Quest is better in a few ways because it offers a challenge, but it rarely evolves from what it excels at(making me think Nintendo is the actual developer), and that's the archaic turn based battle system we all know and love. Dragon Quest also offers more diverse features. In Dragon Quest IV you follow the chapters of different characters and then they all meet up as opposed to standard Final Fantasies where you control one character through most of the game. In Dragon Quest V you actually get married and have kids, as opposed to Final Fantasy where it happens in the end, if at all. You could say that its charm is that it's simple, but I really prefer a game that emphasizes story and character development.
I'm not saying the Dragon Quest series is bad, I'm just saying that it is inferior in many areas when compared to Final Fantasy.