It's been a long time since I played through DQ3, but I remember finding it a more complex game than FF3, especially when it came to cross classing characters, which I loved. I also appreciated the game's use of the night/day system, and how much more exploration was involved in the game, with the orb hunting coming to mind in particular.

That said, though, I do generally prefer FF3. I liked the music more, the ease of shifting classes (especially since I didn't revert to level 1 each time), the pace, and the dungeons were more memorable to me. It's also a bit unfair for DQ, but growing up with the FF series I also loved seeing summons come into the series, especially the boss battles with them beforehand, and vastly preferred the side view battles.