[RM2K3] HOW TO MAKE A FUN AND SIMPLE ATB SYSTEM?

you don't

Wait should be set to ON (and by default) because not many people really care for making split decisions during strategy, though in general rm2k3 just has a bad game feel when it comes to doing an action but having to wait for an enemy do its move (this happens with wait on regardless but it's less noticeable if the agility score isn't equal)

If you're using the cherry based RM2K3 (the official commercial one) then the agility/atb speed values should be bearable, but just know that agility is a really fickle stat and shouldn't be messed around with too much. If I recall 1 monster with double agility than the hero will act twice for every hero turn, this gets complicated by the amount of actors there are. I don't know if its changed with the official version. I would do a lot of tests similar to this and also don't even level it up or bother making it modifiable if it becomes a hassle.

As for making it actually fun from a strategic standpoint: I would actually just focus on things like target priority, which monster is a threat? Then which skills will actually target those monsters, maybe there are multiple biggest threats but they're taken down easily by AOE, maybe worst threat is invincible but takes poison damage, maybe the biggest threat only casts magic so silence is the best choice (and obvious to do), maybe just attacking is the best bet but the next one down the threat chain further requires magic/elemental weakness. All it is just "What can I target" and "What skill can I use" and making those choices interesting (and not a super dumb guessing game). When to attack and when to heal is also it's own binary split choice since healing is same as targeting but more of a reactive whack a mole (but only with multiple party members).

One thing I would avoid the most is the enemy using stuns or slow or any of that since it makes the ATB side really bad. I would emphasize to just keep Agility super static and tuned to monsters attacking when you want them to.

There's a decent guide by Craze that breaks down the number crunching and gives some advice: https://rpgmaker.net/articles/371/

There's custom battle systems that need a custom menu too, because the use of items on battle.
Atleast for make turn-based battles.