Phantasy Star and Chrono Trigger had special spell combinations, where multiple characters would work together to cast a single powerful spell. Phantasy Star did this better imo; the combinations were generic, so you could substitute one characters fire spell for another when the party changed, and it also required timing the attacks properly. It even included a macro system to set turn order to facilitate this, which also made random encounters a lot faster, as you could select an appropriate macro instead of manually entering commands for each member.
Suikoden had a system whereby the animations for attacks during combat would happen simultaneously provided it didn't cause conflicts. For example, 4 people could attack a single enemy at once, but if the first person killed that enemy, then the other 3 would attack different enemies, again, at the same time, unless say, one of those secondary enemies needed to attack first. It all felt incredibly fluid and realistic compared to other games with turn based combat.
Suikoden also had an excellent system for avoiding combat- depending on your relative power level, the command would change from 'Flee' to 'Let go' and there was also a bribery option.
FF10 had REAL turn based combat, where each individual character took their turn as rapidly as their agility allowed, instead of everyone simply getting one action per round of combat. Some other games do this as well, but honestly, it should be way more popular. It's the best system by far, allowing for different speeds of monsters, characters, and even individual actions.
Star Ocean and the Tales series allowed for gaining proficiency with the specific spells or skills you actually used during combat. At certain benchmarks, the skills could change radically, gaining range or area of effect or multiple hits, and the system was also linked to learning entirely new moves. Was a lot more satisfying than generic stat gains from fighting, and added to replayability because you could end up with totally new skills by playing and using different stuff next time.
Lufia 2 had by far the best implementation of a limit break system in any game I've ever seen- it was linked to equipment, such that every equipment slot potentially provided it's own limit break for the character. They varied in cost as well, so during battle it was an important resource to manage since it only built up when taking damage, and you had to gauge whether to use a powerful skill costing 100% of your bar, or perhaps frequently using lesser ones. It made the equipment far more interesting as well; since an armour might be inferior stat wise but grant a superior abilitiy.
Breath of Fire 3 had a universal blue magic system, where any character could spend their turn observing an enemy, and if the enemy used an applicable skill, the character would learn it. You could later transfer these skills between party members as well.
BoF3 also had a brilliant transformation system, where you could select up to 3 'genes' to fuse together to create a dragon form. Aside from some obvious effects like elementals or stats, there were interesting meta modifiers as well, such as reverse, and unique combinations could create special forms. It was very fun to experiment with and gave a ton of options in battle.
BoF5 had a very cool resource in combat that was used to enable an overpowered transformation; however, this resource could never be restored for the entire game, and had a few other uses as well. On top of that, running out of that resource would cause an instant game over. It made for some very tense decisions of when to make use of it, considering the game also limited saving so you couldn't easily save scum and change your mind.
Vanguard Bandits had a system where you could actively choose how your character would respond each time he was attacked- whether to dodge, block, counter etc. Some options would be restricted based on positioning or stamina levels. Very cool.
Tales games have had a grading system for a long time, where your performance in combat is scored and you can get benefits or rewards for playing better, such as using correct elements to attack with, avoiding damage, finishing quickly, refraining from using consumables, etc. The better versions include a balanced variety of factors that allow different types of play to be rewarded. Another system in a similar vein is to chain battles on after another to increase rewards. This can add a cool risk/reward factor, pushing the player to keep fighting while resources are dangerously low, rather than simply resting.
The SaGa series allows characters to learn new skills during battle, especially in moments of high tension like a boss fight or while most of the party has fallen. Makes for a lot of really cool moments, and experimenting to figure out which conditions lead to learning which skills can be fun.
Another feature of the SaGa games was LP: Characters had a (typically single digit) stat that determined how many times they could fall in battle. Getting them back up only required basic healing, rather than special revival spells, but LP was typically impossible to restore in combat and was lost not only when they lost their HP and fell unconscious, but also if they were hit again while laying on the ground. Made for some interesting priorities in some battles.
Valkyrie Profile had a combo system, where chaining people's attacks together properly built up a meter that allowed for powerful finishing moves. There were other effects as well, like juggling an enemy in the air granted a special resource of some kind, and some enemies had to have their guard broken by heavier attacks or being surrounded.
Crystal Project lets you see what attacks the enemy has available, including precisely how much damage they deal, and indicates which move they are going to use and on who. It makes for much more thoughtful combat, as exploiting enemy behaviour with the threat system or clever defenses or counter attacks, is a huge factor in playing well.
