I suspect the Kha'ak were resurrected and reinstated as the Xenon and pirates were too little of a threat to the player,

I can say X4 did put more work into playing story lines. Most of X3TC's plots really summed up to the PHQ plot, and X3AP added an easy to ignore war that mainly amounted to more ships shooting at each other in contentious sectors. While the story was there you had to imagine a lot of the goings on in your head. X4 has more dialog, cut scenes, and direct interaction involved in the available plot lines -- though many players don't appreciate that a lot of them are not skippable (like your lost Boron friend in the new PHQ plot who -will not shut up-).

Like the Split (added in Split Vendetta), Terrans (added in Cradle of Humanity) and the new pirate/smuggler factions (introduced in Tides of Avarice), the Boron are to be reintroduced in the upcoming Kingdom End DLC scheduled to be released later this month (finally!).

Edit: And yes, they're basically gated behind gates that have not come back online

Nope, all gone. But nothing stops you from naming them as such.
Like in X3, I think most players still use naming conventions to keep their ships sorted in the fleet menu.
Sort options and filtering really haven't improved much in that area.

For the most part, yes, some babysitting is still required.

Ship orders have gotten significantly more complex -- or perhaps I should say the menu navigation required to set them has gotten more complex, and what each order does is not exactly well documented. Technically, if your resupply ships have all of the necessary blueprints available and build resources aboard, and all of your homebased wings have their orders properly set up for resupply, they should rotate back as necessary. In my experience, they do head back when they need more ammo/missiles, but rarely turn back for repairs early enough to avoid getting blown out of the sky. But hey, I may not have all my orders set quite right! (it's hard to tell ;)

One nuisance I can say, though, is that if you've got a carrier holding 110 S-class ships... you're going to have to set those orders up 110 times. There's a Mimic order that takes care of some of these things, but even in that case, the Mimic order needs to be set on each applicable ship. Theoretically you can select a group of ships and set all their orders at once. It mostly works, but is still a little hit and miss due to some orders only being available to, for example, a 3+ star pilot or only a certain sub-class of ship.

Edit: Come to think of it, a lot of the above doesn't apply to resupply, because resupply is a ship setting not a ship order XD

I was referring to the TM class ships from X3TC/X3AP -- Split Boa, Yaki Chokaro, etc. -- they're nowhere to be found.

I play for the space trade sim / empire building / ship capturing aspects of the game (and the scenery).
The story is just a nice back drop to align my game start with my chosen role play for that session.
You're far more into the lore than I am ;)

I can't say. As a game dev myself, I always try to play things unmodded for the first hundred hours or so to get the intended developers' experience. If it's not good enough to last that long then I won't bother modding it.

In the case of X4, the only mod I've applied is one that stops transport ships from flying into an obvious hazard and getting themselves killed for no good reason. I've enjoyed the game otherwise without any modding. Sure, there are annoyances, but it's the intended experience and I'm good with that.

Though after thousands of hours in X3, I ran through XRM, Litcube's Universe, etc., used MARS fire control extensively and so on. In the end settled on Litcube's + PSCO1 cockpit mod being my happy X3AP balance.

For orders, -sometimes- (again, dependent on pilot level and ship classes in the wing), but ship settings are independently assigned.

With this patch the performance level is finally serviceable for me. Not great, but serviceable. I have a i5-10600k & 3060ti.

I had to quit the game last version because I was tired of the FPS from the unreasonably taxing 3D map. We'll see if it gets that way again...

Agreed, with 6.00 I'm able to easily maintain a completely stable 60 fps at 7680x1440 (triple head) and all graphics options maxed... save for disabling Volumetric Fog that is -- it doesn't play well with the higher MXAA options.

And save/load times are finally tolerable now, too :)

(Ryzen 9 5950X, 3090 FTW3)