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Battle System
Combat
Chrono Trigger - Super famicom and SNES
ATB, magical attacks have an area of effect and enemies are constantly moving, every character has an elemental attack and enemies have elemental weaknesses, there are combine attacks between character pairs or triples.
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Customization
Character stat progression
Final Fantasy V - Super famicom and SNES
Job system + two skills can carry over from another job
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Final Fantasy XII: International Zodiac Job System... - PlayStation 2
License grid (zodiac): it's basically FFX's sphere grid, but slightly more open and affects what you can equip too + gambit system: so you can actually control everyone in your party even though you control only one in-battle.
Final Fantasy VIII - PlayStation
Junction system, you equip GFs and level up skils till you get them. It customizes everything, even battle commands.
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Shadow Hearts: Covenant - PlayStation 2
I feel like every character has a different form of progression
Final Fantasy X - PlayStation 2
Sphere grid. Add abilities to weapons and armor.
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Tales of Vesperia - Xbox 360
Weapons give skills. It's like Final Fantasy IX, but in Vesperia the skills are more useful (in part because it's battle system is action-based) with many skills that you clearly see doing something in battle or you yourself use them.
Final Fantasy VI - Super famicom and SNES
Similar to FFVIII, the summons (espers here) give you the customization, here stats and magic. The characters are all very different and the equipment almost always has some relevant extra effect.

Promising
Yet to play or to play more
The best customization and battle systems I have played. The list'll grow as I play more.