In some systems, turns are determined by a global timer that fills up independently from the battle members. Of course, this isn't always positive, as some buffs that are meant to be short-term last for multiple actions on fast characters and slower ones might not even get to act before their buffs run out.
You can't really base turns on each character's actions in such a system, since states like petrification, which set AGI to 0, will never expire this way.
The 3rd way is setting a turn to be X actions over all characters, which also (possibly to a different extent) suffers from the same problems as a global timer.
There's actually at least 1 more - State Countdown Timer. It can either be fixed x seconds per turn, or variable x seconds per turn(x here can depend on many conditions).
I agree that at times ATB systems are executed really well, but more often than not I've found myself annoyed by them. They're either too fast that you don't get a chance to select commands in time, or they're too slow and you sit there waiting for the bars to fill up. The beauty with fully turn-based systems is that you don't need to do either of those. You're not waiting for any timers at any point.
Another thing that I don't like about ATB is that it's not always clear what the duration of a turn is. Some states might last a certain number of turns, and because in ATB faster characters have their bars fill up quicker than slower ones, the definition of one turn becomes very unclear, which also tends to ruin the strategic gameplay.
The ATB speed problem can be countered by letting developers control the global atb speed and wait conditions, even on the fly.
The turn problem can be countered by showing the global atb clock(with frame or executed actions as its unit), or the countdown timer for countdown states.
Actually, if implemented and used well, an ATB can even replicate a CTB
I personally prefer ATB, as an extremely powerful atb system can do almost anything the default battle system and CTB can do while the reverse is likely really false, and I still can't master the added movement and space control in ABS yet. For TBS, I think it can be combined with any battle system aforementioned, at least conceptual wise.
But after all, I just want to clean somethings up about the ATB, as I think choosing battle systems is up to developer needs and preferences
P.S.: Maybe later I'll open a post to talk about the existing atb system scripts I know so far, but I don't know where that post would belong to(e.g.: RMVXA Tutorial? Not quite a good match lol)