Dragon Warrior 2. DW1 is a rather simple game, with just one character in the party, one enemy, and some very primitive mechanics (though still conventional-feeling, unlike early Ultima). But then you get DW2, which gives you a 3 character party, has you fighting multiple enemies, not to mention a much bigger world with even the addition of a ship to travel the world.

DW3 further added character creation and a class system, so you get to choose your party composition. (Also 4 character parties, as well).

Final Fantasy 5 is a significant improvement over previous entries. Not only can you choose each character's class (a feature found in FF1 and FF3 that's missing in FF4), but you also get to choose a secondary ability from a class you've been in before, creating so many possibilities, far more than in any earlier FF game. There's also so many interesting new abilities, like Blue Magic (which the game gives you early), Sing (Bards are actually useful, for the first time in the series!), Mix, and many other less prominent ones. It really is a shame that FF6 was a step backwards, no longer allowing class selection, and getting rid of some of the more interesting abilities (I'd rather they kept Mix rather than Throw).

I could also mention Castlevania 2, though that game felt like a different platformer sub-genre than either 1 or 3 (and one I wish there were more of).