I didn't like SD3 much. I was actually playing it today. It's kind of slow and gets rids of all the puzzle-solving bits from SD2, where you used your weapons to interact with the environment. It does add a day/night cycle, a weekly day cycle, and class changing, but the first two are more cute than consequential and the latter's just not a very interesting class system.
In all fairness it did have the six characters and three different story lines (even if they were almost identical) versus Secret's almost entirely liner trek (you had a few ways to go about the beginning of the game but after the Witch's Castle you were on the straight and narrow for the rest of the game).
However I too believe SD2 to be the superior game. For instance I still consider SoM's weapon/spell level system to be the best implementation of the idea yet (though they could've done something about charging up for those high level weapon skills). I also adored the wide open areas versus the compartments of SD3. The action gauge to discourage attack spamming versus III's hit gauge that never filled up unless enemies were strong enough to kick your ass. The lack of inventory space in FFA2 along with no rare items (equipment and orbs filled that role however) discouraged you from going overboard on both hoarding and total item dependency whereas FFA3 made it so that with a crappy party you could still do all the essential stuff like status effects and pumpkin tossing so long as you had the cash or were lucky enough to score them from a drop since only one shop in the entire game sold these and only at night and the inventory was limited at best (plus there were so many items to keep track of you had to keep the extras in a separate bag which could only be accessed outside of battle).
Though again, to be fair, you did get to ride on the back of a turtle.