Some things off the top of my head:
FF10's turn based system. I like how it shows you the sequence of turns for each participant. Other games also have turns based on Agility, but they don't show you when your turn or the enemy's comes up. This lets you plan with more precision. I prefer any kind of turn based to RTwP systems like ATB.
If you're gonna have ATB, though, then Chrono Trigger got it right. Enemies are not static, they move around in random fashion as your bar fills up. You have to take enemy movement into account when using AoE attacks, such as those that attack in a straight line from your character. You can hit several enemies with a single attack if you time it correctly, but doing so involves wasting some of your bar. This is the only reason to have ATB, imo.
Chrono Cross added an elemental layer to combat. The more an element is used, the more powerful it becomes. Since each character has an innate elemental alignment, this can turn into a decisive advantage or disadvantage. This forces you to pay attention to something other than healing and damage. Even if you set up proper defenses and healing adequately, an enemy that has taken control of the elemental alignment may use a more powerful attack that overwhelms your defenses.
FF8 lets you equip spells in the form of junctions. A fire spell may reinforce your strength, your elemental defense against fire, or your elemental attack. This system was criticized because you had to draw spells from enemies up to a maximum of 100, a repetitive and tedious process. You could simplify the system by having just one of each with the same function. I actually like FF8's system of spell accumulation, although I prefer to refine them from items.
FF8 had the best idea for a bestiary, an addicting card game where each card is represented by a monster. Generally speaking, the more powerful and rare the monster, the more powerful, rare and valuable the card. You could further convert cards into useful items and spells, a perfect gameplay loop.
Vagrant Story let you fuse equipment in the manner of a monster breeding game. You can spend many hours forging your own equipment from all the pieces you gathered. In addition, equipment could be made of several materials which serve as modifiers in the way of roguelike games, something I always like to see. You could also increase the affinity of equipment by using it against a certain type of enemy. I like the idea of a shield you use against undead, or reptilians, not because it comes with a +1 for that, but because you made it so.
