Rato's Rebalance is a good mod. It adds a directional stance to weapons where firing at the same/close by targets requires less action points than shooting at targets outside the merc's view, a recoil system where strong characters have an easier time keeping their aim on target, full damage to autofire but increased critical hit chance for single shots, a short-range malus to scoped-up long distance rifles, bigger awareness cones around enemies to discourage overpowered melee kills, and plenty of other stuff. I would only recommend it after reaching the halfway point of normal JA3 first.
Smart Overwatch is useful. It stops your soldiers wasting their overwatch shots on impossible attempts at the target's torso and instead aiming for visible body parts. You can also manually set shot types and targets for overwatch.
I think the... uhh... Exit Wounds(?) option when starting a new game incorporates similar bleeding penalties as the defunct Bleeding Mod. It was introduced in 1.4 or 1.5.
Pinned Down is a good addition too. It causes your mercs and enemies both start losing action points from just getting shot at. Not sure if the Nexusmods version is still compatible, the one in Steam Workshop is more recent.
As for just QoL stuff, I like
Interface Tweaks that adds all sorts of sensible ideas to the UI, mainly in the inventory. There were also
SAY THE LINES -mods which cause all applicable merc banters to fire when there's a trigger for it in the conversation so you'll have multiple dudes interjecting when they have something to say. That one probably doesn't work in the current game, unfortunately.