The ones immediately coming to mind are:

Parasite Eve

Eyyy, Edge beat me to this one. Although it is actually a weapon/armor customization system I'd say it counts, as those two pieces of gear determined virtually everything about your character. I really liked the way the game implemented this, as your equipment was almost like a character beside your character that you were improving the whole game, and there were even items you got that specifically boosted the stats on your gear. Even better, because of the limited ability to move stats and abilities around with Tools, finding new equipment was always exciting since you never knew what new property you might find or, due to the destructive nature of migration in the title, finally be able to get back. You also had limited slots to drop what you wanted into, so you almost always had to make choices around some kind of restriction; it made your choices more important. It also made Super Tools pretty much the hypest find in the entire game, because you had the rare opportunity to migrate things without having to make that choice, which was an awesome feeling. I get to keep my +20 damage AND my freeze bullets? Yes, please. It also made the Chrysler Building feel less tedious and (almost) rewarding, as you could find all those rare trading cards there and make the super awesome dream gear you were effectively locked out of during your first playthrough. It's too bad the second game opted for a completely different take on this, focusing on Aya's actual customization, because it wasn't ever as interesting, especially as I really don't remember upgrading anything other than magic in that game.

Romancing Saga 3

Outright, Romancing SaGa 3 has my favorite character customization in any RPG, as you can do pretty much anything you want with any character, but opportunity cost is the name of the game; you'll either need to think creatively or give characters special gear/formations for them to really shine where they don't naturally excel. As an example, Zo is a massive elephant man and miles away the sturdiest member in the cast, but you can make the dainty princess Monica or wispy mage Undine your tank instead, and they'll do it well enough, you just have to customize both them and your overall strategy to make it happen. Loading Monica with heavy armor and shields like you would with Zo can work, but you'll probably also need to hunt down con boosting equipment for her as well if you go that route, and shift your formation -- a change that affects your entire party -- to better accommodate her. Or, alternately, you could place her in lightweight gear and put her on point in a formation like Desert Lance with evasion / counter techs, so she is faster and draws additional aggro. There are just tooooons of options and choices like this you can make when developing your characters in the game, and I love it for it. It's probably the reason I spend more time playing RS3 than FF6, despite actually liking the latter more as an overall experience. Speaking of . . .

Final Fantasy VI

There are a ton of customization options in this series, ranging from super minor like in FF I and IX to damn near complete tabula rasa like in FF2 and Tactics, but FFVI ends up having my favorite for reasons somewhat similar to the above RS3 -- you have relative freedom tempered by defined characters. Princess Monica is not Zo; Cyan is not Realm. But both can do what the other does, largely, if you are willing to make the investment in it -- hell, Cyan is actually a more terrifying mage than Realm is when you play him with a Genji Glove and dual Kazikiri/Tempests, and that's not even getting into the silly of Merit Award Gau with the damn things. There are just so many unique and interesting things you can do with your characters within their own already set boundries. I also like the way the game facilitates this, as Relics are almost always exciting finds as they allow for immediate augmentation, while Espers provide a goal you are working towards with long term benefits. It is actually a bit similar to what FF5 achieves with its job system, as you can swap to being a monk for all your monk perks whenever you and slowly work towards permanently unlocking those abilities by using it, but 6 allows me to just have my bonus without changing who / what my character is, and I prefer that. I can equip earrings on Edgar for bonus damage when I want to use Flash without having to be a mage. Similarly, I can't simply make Edgar a Ninja whenever I want to throw things; that is not a thing he does. I have to work with what I have and mold it into what I want it to be, with a small scale ability to trade in perks on the fly, as opposed to being able to wholesale shift what I have whenever I want. It limits my choices and makes them feel more interesting and significant, and I like that.

Front Mission 3

Customization, as a whole, is the name of the game with Front Mission, and I'd be hard pressed to think of a series I feel has achieved it better across its main titles. That said, while FM5 has the most depth to the system, FM3 is my personal favorite iteration. I like being able to upgrade parts instead of having to constantly replace them; I like that can parts can teach any skill to any pilot, so characters never feel 'locked' into a certain role; I like not having to worry about friendly fire due to character personalities; I like being able to steal enemy wanzers to upgrade my own units; I like that I can make a team of nothing but heavy shock units and have it just as viable as a balanced force and that there are ups and downs to every loadout; I like the impact/pierce/lastTypeINeverUse weapon triangle. The game just has so many options I prefer over the other entries in the series.


Ring of Red

Customization in Ring of Red is a lot like in Front Mission, only completely different. Your mechs are completely static in the game, minus story upgrades, as are your pilots and the skills they learn, but your ground units are not, and it is through them instead of different parts that you customize your characters. Each mech is supported by three squads of footsoldiers that come in six classes and all have unique properties, ranging from increasing your reload speed to firing off white phosphorus at enemy ground units to disable them, and the way you pair these units with your mech changes how you fight completely. Kinasato, for instance, is a light, evasive unit designed to harass (see also: brutally murder) enemy ground troops, but nothing stops you from loading him up with smoke shots and grenades and running straight into an enemy mech's face to rip them apart, or loading him out with wires and cleanup crews and using him to lure enemy units and flee from them; you can run double flash shots and attempt to prevent the enemy from ever shooting with careful troop cycling, you can run advanced mines and try to bait melee mechs into swinging at you -- there are just so many potential options. And all (almost -- melee John is a bad, bad idea) of them are completely viable, each with downsides you have to contend with. Even better, much like eject punching yourself Wanzer parts in FM3, you have to actively hunt down the best ground troops in the game by completing certain goals during missions, so your reward for good customization is even better customization! It's just too bad Konami never continued this series, because it could have been as good as FM if it had the time to develop more.