I replayed the entire crisis, start to finish with the B6 updates. Unfortunately for the most part my original impressions still stand.
Additional thoughts after the second time playing through the crisis starting fresh in B6:
1. Introduction to the crisis mechanic
This is a marginal improvement of B6 to how things were before in that the research and initial introduction to the CPU ship is at least slightly better than nothing (and opt in). I do think the signposting could use a little more creativity and be less immersion breaking. There are so many ways to do it, too (e.g. something like "I've discovered a dormant signal that matches Xenon signatures, messing with it may be a bad idea, but let's do it anyway for SCIENCE"). You can signpost things in a way that are still obvious to anyone with a brain without putting a little red OOC note that says "click here to trigger game mechanic". For anyone else contemplating replaying the crisis with B6, this is the only change to the writing/depth/explanation of anything.
2. The crisis itself
I don't know how much of this is random/chance, but these are the changes I've noticed the second time around:
2a. Progression
After the introduction and initial incursion of Kha'ak + Xenon, I had ten hours worth of incursions that had no Kha'ak whatsoever (other than the little Forager) with the exact same 3K+1I spawn over and over again. This is incredibly tedious and grindy, to the point where I wondered whether the game had broken. Then I had just three (or four, maybe?) full on Kha'ak incursions which were over fairly quickly before the CPU ship hunt began, concluding the crisis.
This seems pretty backwards in terms of pacing - you'd want the more interesting part taking up the largest portion of the experience, not the other way around.
Concluding the crisis with finding the CPU ship which is alone, unguarded and doesn't even fight back also feels like a big letdown. You'd expect the crisis to end with a huge climactic fight or something (especially after Boso tells you to bring enough firepower), but nope. Just make it to the inert decorative CPU ship before it randomly jumps away and The End. No explanation, or aftermath, or anything either.
2b. Mechanics
Incursion fleets seem less magnetised to player assets and will actually attack NPC factions as well. This is good.
The Xenon seem to spawn further afield than they did in earlier versions. On the one hand this is "good". Even though they're still spawned out of nowhere, at least it's usually out of sensor range, so feels a little less contrived. On the other hand, this presents a problem with these initial waves: They're on such a tight timer that it really is just a game of whack a mole. "Observing the Forager" is basically pure luck at this point since there's no indication whatsoever where the group of Xenon has spawned, with the event concluding before they make their way into the sector proper. I'm still not clear whether doing so actually affects anything or not.
Another issue with this is that sometimes the Xenon just forget what they're doing and sit there, out in the middle of nowhere. You'll get the defend mission but the Xenon never show up. If you don't hunt for them and find them in time the mission will fail eventually, even though you've never seen a single Xenon (and they certainly haven't attacked anything).
The problem of Boso living in a parallel universe still persists. He'll happily ramble about President's End (which should not be a repeatable line of dialogue) and how destructive the Kha'ak are over and over (and worse, how they've "stopped the attack"), through ten hours of not seeing a single one of them besides a solitary Forager. Later when hunting the CPU ship, he will find the mysterious signal for you to investigate. If you don't make it in time, he will somehow intuit that "it's charging a jump drive", and the next time he will cheerfully tell you he's "found the CPU ship again", even though you might have never seen it beyond the introduction.
Again, having an indestructible hostile asset just hang around is a really bad idea, if you recall the issues with Kha'ak installations in earlier versions of the game. It also does not make much sense. How about instead allowing us to strip down the wreck of the CPU ship, and have that be the unlock for capturable/bailed Xenon ships and blueprints? That would at least make more sense (reverse engineering the CPU ship to understand Xenon control circuits/signalling), and make the addition of those features in 7.0 more fun/immersive.
On the actual Kha'ak incursions, it does seem like the Ravager spawns are a little less cheap (i.e. not spawning directly on player assets), which is another improvement. The timer on the combined incursions is also a lot more forgiving, so they're less frustrating than the early waves.
Achievements seemed to work this time.
2c. Location
The initial Xenon-only waves were pretty much the same as last time - it feels like spawning in each of your sectors with assets in, from largest to smallest. Since they spawn further away now, this is fine.
The combined incursions seem like they were changed. The inital one, right after the introduction was in a seemingly random PAR sector I didn't have anything in. Every single one in the course of the actual crisis (after the slog of Xenon-only ones) followed the same pattern. They'd spawn in systems that I might have ships in, but never in a system that I had any actual stake or stations in. I don't know if this is on purpose (to avoid fights near large stations). The first one was deep in the Boron core sectors, which meant scrambling through Sanctuary of Darkness and the other ones. I had another in one of the Windfall sectors which I'd cleared out of VIG, so there was basically nothing in the sector at all. The last one was in Asteroid Belt, which again, I don't have anything in.
2d. Balancing
Having played the crisis a second time, I really get the feeling it's balanced to be a single, player-piloted, ship adventure (from the need of the player to be personally involved every step of the way, to the scale of incursions). Which is... fine, I guess, but it's not really what the feature purports to be and a letdown as far as late game content goes. You could complete the crisis just as well after capturing or buying your first few destroyers, a few hours into a new game.
The initial Xenon-only spawns are not a threat in any sense of the word whatsoever, and they're all exactly the same. It'd honestly be an improvement to remove them, or perhaps limit them to one or two events.
The combined incursions are a little more interesting, but again, hardly a threat to any of the established factions, much less a player with significant infrastructure.
The only 'challenge' as far as the crisis goes, is magically knowing to have your assets in the right place. For the initial Xenon spawns, just parking some destroyers in every sector you have stations in largely solves that issue (though actually finding them might be another as previously mentioned). For the combined incursions, it's basically a scramble to move all your ships out of the sector and blacklist it (which is a major pain as it doesn't apply to current orders, so you'll still have suicidal traders/miners trickling in) and then get the nearest destoyer(s) there.
Throughout the experience, I never lost a single capital ship to the incursions, with the only losses being civilian ships that I struggled to tell to keep out of sectors. It's more of a fight with game mechanics than an actual enemy in that sense, which is not ideal.
Overall feedback on B6:
I can only refer back to my original feedback and suggestions for improvement. Please listen to the feedback from people in this thread and go back to the drawing board on the crisis. I don't think more development time sunk into what you have right now is going to address any of the fundamental problems with it. Don't rush an implementation in 7.0, and don't let the potential for a true late game challenge which actually leverages core X game elements succumb to a sunk cost fallacy.