I'm not a big fan of the ATB system von a lot Final Fantasy game, so for me the best turn based system was a long time the one of Final Fantasy X. It's rather simple having enemies with up to 4 weaknesses and a good system for different alligments for the enemies and resistences. I also like the progression bar that show the action order of friends and enemies. So speed makes a difference. I would still say it's good, but not the best anymore for me.
The best two system for me are not really surprising. One it the one of the Trails of Cold Steel games (i haven't played the newest trails game yet). Adding the area as another factor gives you more possibilities for strategies. So go with more tanky (or fast) characters while the more offensive stays back helps a lot. Also there are enough possiblities to buff defense when a McBurn in the second game just one hits the team. Positioning, buffing, healing, making dmg, they have just done a good job with it. The only downside, it's to hard to break but the 3rd and 4th game have some limitations to present it a bit.
If Trails of Cold Steel is cheating for you because the area doesn't make it a classical turn based game anymore i would say most of the battle systems of Atlus are very good. Regardless of Persona, Shin Megami Tensei or another spinoff, the base of the game with different elements and buff or debuff is often the same. Atlus keeps their games interresting with always different additions to their gameplay. Persona 5 has maybe one of the best for me with baton pass and more addition the futher you get into the game. But i also liked Tokyo Mirrage Session a lot.
I LOVE Shin Megami Tensei's press turn system. On critical hits, or attacks that the enemy is weak to, you essentially gain an extra turn. It really encourages you to build your team wisely, with a large variety of spells.
Persona changed it a bit with the One More system, and it's very similar.
Just started playing it, but I’m loving the combat in Sea of Stars. You get that traditional JRPG turn-based combat, but you also get “skill-based” timing to do additional damage or block some damage. That and the way they handle the turns, and the ability to “stagger” with different attack/magic combos makes the combat very engaging
That was already a long approach of mario rpg games, but that's also the reason i avoid them. I don't really know if i wouldn't like it since i haven't played such a game, but i will with sea of star or mario rpg for sure at some point. But i guess just good a strategy and don't care about messing up some timing things is rather my way to go.
Seconding Final Fantasy X and Trails. Turn-based systems that remove the concept of turn cycles governed by rounds are great. These systems allow for speed stats to actually mean something and make things feel dynamic even though there are pauses every turn. It's so much more interesting to give a ninja-like character multiple turns instead of multiple attacks to present the illusion of speed. The Atelier games have a similar system too (although I've heard Ryza went to something like ATB now).
If we're including ATB and ATB-like systems, Final Fantasy X-2 and Panzer Dragoon Saga are my overall favorites.
I don't know if there can be a best, but yeah, the Trails games being effectively ffx, but with positioning and even faster is so satisfying.
But then you can go way back to ff1. That battle system is flawed, to say the least. But once you know the ins and outs you can really push it in fun ways.
It's good to mention radient historia too, making the entire battle system be about positioning and moving enemies around on a grid was super fun, it just starts to get really puzzly and fun by the end
But the actual answer if I had to pick goes to Etrian Oddyssy, any of them. When you make a modern game and base it entirely around dungeon crawling combat, the gameplay better be good. And they just nailed it. It's the perfect traditional line based combat it really is. Job systems to keep things fresh, a lot of strategy and the game will kick your butt if you just go in and push attack
Final Fantasy X and Shadow Hearts Covenant have had my favorite battle systems. Especially Shadow Hearts since the judgement ring is a good combination of strategy and skill.