Since I can't think of anything from the games I am currently playing to write about, I guess I will borrow my brother's idea of writing about older games that I like. In this case, one of Square's last RPGs for the Super Nintendo: Chrono Trigger. I can probably write a lot about the many things I like about that game, but I will start with the Dual and Triple Tech system.
In Chrono Trigger, each of the seven characters has a list of only eight special techniques they ca use in battle other than the basic attack and item commands. These lists are fairly specialized for each character, with each character being (with a few minor exceptions) being limited to a single element and a limited number of roles (such as healing, physical attack, or magical attack). Also, it is impossible to alter this list or customize the characters in meaningful way, so your only choices of how to customize your team is through choosing team members. However, because of the way Chrono Trigger embraces that concept, the system is not limiting at all.
The biggest strength of the Chrono Trigger system is the way it makes the classic idea of choosing a few people for a battle team from a larger pool of characters and turns it into something far more than just picking characters to cover every role that you need. In a typical RPG that allows character choices, so long as you have the basics of survival (healing and defense) and attack covered, character choices do not depend on each other. For example, in Breath of Fire 2, choosing between Nina and Bleu, who are both mages who use attack spells, is simply matter of personal preference, and won't affect the rest of your team. However in Chrono Trigger, while both Robo and Ayla are primarily physical attackers, the choice between them is decided by more than just personal preference, because of the Dual Tech system.
With the Dual Tech system, combination of character affects your team's abilities just as much as character choice itself. For example, the choice between Robo and Ayla when Crono (lightning attacker) and Marle (ice healer) are already in the team. Choosing Robo not only adds his own physical attack abilities to the team, his Dual Techs with Crono enables powerful wide-area magical attacks, and his Dual Techs with Marle brings some very strong full-party healing moves to the team. On the other hand, Ayla's Dual Techs with Crono enable powerful single target lightning attacks and wide area physical hits, and her Dual Techs with Marle give a powerful stealing ability and strong ice attacks. The choice between Robo and Ayla affects the abilities of the other characters. With certain combinations, this lets characters do things as a team that they can not do individually under any circumstance (such as ice mage Marle and fire mage Lucca using Shadow elemental attacks).
In essence, Chrono Trigger sacrifices individual character flexibility in exchange for much greater flexibility of the party as a whole. Choosing the party is the very same thing as customizing your characters. It embraces the idea that choosing members for a team is an important choice, and has an elegant system for rewarding good choices in party composition. I think this is a huge improvement over many other RPGs, where the choice of team members is redundant because of the freedom to customize characters individually (such as Final Fantasy 7 or 8, where you choose a party of three characters out of a pool of 6-8, even though each character is infinitely flexible in equal ways), or where the choice between characters is no different from merely choosing a list of abilities you want to bring to a battle.
Unfortunately, the concept of a deeply integrated system of character synergy affecting team selection has not been imitated much by later RPGs. A few RPGs have used it to a limited extent (such as the Unite attacks in the Suikoden games), but they do so more to encourage specific plot-related combinations of characters rather than provide a way of making every character combination unique. Even Chrono Trigger's sequel, Chrono Cross, failed to effectively make use of such a system. However, the quality of the concept is good enough that I imagine it will resurface eventually.