This is really looking great, Alex! I like pretty much everything I see in these changes and I am really looking forward to seeing how the "combat funnel" gets implemented
Spoiler
1. The level cap and leveling in general are going to need to get looked at, I think. I'm in agreement with Megas there. We're already squeezed to the point that players got pushed into some pretty squirrel-case builds, and I think that's significant. I'd prefer a return of the soft-cap, both for players and Officers (or at least let Officers fill out their skill-bars).
2. I certainly agreed with everything you said in defense of the improved early-game experience vis-a-vis the "Tutorial" scenario.
However, I think a couple of things might be improved.
A. The early-game power-curve needs to be faster, so that players don't hit a wall quite so fast.
In the private build I play, I have the experience at roughly 8X normal right now, which demonstrates this in a way that I think you might want to playtest (essentially, unless you're an expert player, you go from, "I'm barely powerful enough to take down weak Pirates" to "I cannot possibly take down the generated Bounty encounters unless I am not only expert but am thoroughly cheesing in every way".
Then, when you're past that plateau, it becomes Easy Street; there's a definite tipping-point right now where I feel like players get a huge hand up about when they can start affording Capitals and have collected enough of the least-balanced weapons, which, depending on how badly you abuse the Factions (especially the Perseans and Tritach) leads to some seriously-amusing power imbalances (a really optimized fleet tears through Pirate bounties very very efficiently because they don't improve other than numbers and remain squishy, while the Deserter fleets remain relevant until later in the curve, among other issues).
In Vanilla, this is considerably easier to reach (the balance changes I've made generally make this a lot harder on the player, because there aren't a lot of things that can be easily abused, now that I've adjusted Variants to take advantage of the changed things).
I don't think any of what I'm saying here applies to Average Joe Player, mind you. Based on what I've seen on streams lately, there aren't that many people doing this kind of thing well; sometimes I wish I had enough spare time to make videos on How To Break Things. But be aware that if the game's played right, the power-curve is still not quite tuned right in late-game.
I'd recommend, at the least, having Pirates get a big upgrade somewhere around Level 30 that gives them new Variants that aren't quite so squishy, or a plethora of highly-leveled Officers, or both, so that it's not quite so easy to amass giant fortunes through Bounties once we're past the middle game.
I'd also recommend that any serious attempt to take over the Sector result in big enough fights that the player won't want to try it until end-game.
To keep the mid-game plateau much more reasonable, I'd suggest a pretty modest reform: increase the System Bounties by enough that a player can actually make a living and make progress by taking them down. They simply don't pay enough right now to be worth doing, and whether or not it's "obvious" to long-time players like me that you're not supposed to do that, I strongly suspect that's what most players will do anyhow (and they'll get frustrated when they cannot make progress into midgame). Perhaps this should use a scalar curve so that the payouts get smaller as the player's power grows, but it probably doesn't have to; when we reach the point where we want to go to the next level, we're talking about enough difference in payout ($250K bounty-head vs., say, a $50K System Bounty for a Pirate "armada") that players will gravitate that way anyhow (at least, that was the effect over here; there's a point where earning $30K is nice if I want to buy Supplies / Fuel, but is almost irrelevant to making progress towards end-game).
B. Late-game, the problem is largely that the player has resources, and nothing to spend it on. I know we're about to see big changes to that, and I'm glad, but I think I should maybe make it clear where the issue is. It's not just "my income vastly outpaces my expenses"; it's also, far too often in Vanilla, "my income has absolutely nothing worth being spent on"; when we pass through the midgame, it's suddenly a game of waiting, fruitlessly trying every Market in the entire Core to buy <insert minor power tool>, etc., which is a real drag now and will be worse if we need a million-plus credits in monthly income to deal with endgame economic expansion, etc., etc.
My last run of pure-Vanilla, I had somewhere on the order of a million Credits by the time I hit Level 30 and there was literally nothing worth buying with it, because too many of the things I actually wanted were behind various walls or were simply not available at all (I mean, really... I have a million credits, can I not simply bribe some Tritachyon corporate officer to let a few things fall off a truck?).
I'm not really a fan of the current system, where we shop endlessly in RNG hoping that something we actually want will drop. It lacks that nice feel Blizzard achieved with Diablo II, where you might have those problems with the shops, but you had the Gems to keep pushing you forward, etc.
One of the few things I actually liked about SPAZ 2 was their "ordering" system, whereby players could buy whatever they needed, including customized gear that put them into a new place on the power-curve. I would like you to perhaps consider having some "+1, +2" etc. mechanics and Uniques that can be gotten by players by doing <insert very difficult thing>. Maybe you could consider making these kinds of things one of the ways AI Cores can be spent?
While I fully expect that Crew pay-as-a-drain will help this impression a lot, I suspect it'll be not nearly enough, and we'll have the same problems Mount and Blade did: the player has resources that cannot get used, efficiently or not. The problem there was that, due to relative power imbalances with troops and putting the best troops behind leveling pay-walls, it became an issue of the level-grinding your troops over and over again to have end-game power worth mentioning.
Here the issue is that with the strict caps on Officers and fleet scales, we can have ideal fleets pretty early and then there's no ceiling to break through.
One idea that I'd like to propose is that non-combat (i.e., stat-only-unless-Iron-Mode) ships aren't subject to the fleet cap at all, and that the cap of 30 be made soft, rather than hard.
The no-fleet-cap-for-civvies idea has a lot of appeal to me, because it gives the player a lot more room to grow and also encourages the player to try doing improbable things with the civvie stuff that might as well not really exist right now. For example, it's amusing to think about players throwing out a fleet of Prometheus tankers with hangers as a desperation move, after their main fleet's lost its CR in a big fight and the enemy has just a few weaker ships to hold the field left.
One good way to limit soft-cap fleet expansion might be to dial back fleet speeds at best-Burn, rather than simply gearing up costs; if you want a fleet of 60 giant capital ships, maybe you can do that, but you're limited to Burn 14 at best speeds, for example, just like the old model for Burn. This is more-or-less how Mount and Blade handled this issue and it largely worked out. We're already fighting against AI fleets larger than us and there's no reason that can't be pushed out further to keep this from feeling ridiculous, in terms of player power. I'd expect, if trying to invade Jangala, for example, to meet a fleet of 200 ships, so I'm OK with players having to juggle 60 they've maxed out and fighting out a battle that takes an hour (over here, I see scenarios like that play out, and so long as performance doesn't tank due to the stuff we've talked about before, it's quite epic and feels utterly satisfying, win or lose).
One thing I do not like about the current optimal strategies for play is how Missile reloading as a CR trade has become such a popular late-game tactic. I feel like that has pushed players into very un-natural and silly builds for fleets. I don't do it, personally (I feel pretty strongly it's still sub-optimal play and Megas is largely right about where balance shifted) but whenever I see that in a stream, I cringe; it feels like an exploit and it illustrates pretty perfectly why limited ammo has been such a problem for sane discussion of balance in the game.
3. The one big worry I have, given the outlines of the current system as you're developing it, is that AI Cores sound like a show-stopper resource. Please, tell me that, if we're willing to spend outrageous amounts of money, we can get more, even if all of the Domain stuff is scraps and every single Remnant has been hunted down? I really dislike the idea that we'll be purposefully farming Remnants in late game just to get Cores because it's the only way; I can <shudders> imagine having to build a Core Farming operation where I've built powerful defensive bases in all the nearby Systems just to keep the Factions away.
Honestly, where the Remnants are concerned, I'd really rather that they go exponential sometimes if nobody keeps them in check and can't be totally eradicated; it'd be much less frustrating if they aren't a resource I carefully farm, but are an occasional major threat that (however briefly) unites the Sector and presents major problems to a player whose mini-empire is in their path. I like the idea that they're the "barbarian horde" at the high end; right now they largely feel like an easy resource target that I have to husband carefully if I want to keep getting Cores. I realize that, for a lot of players, they're considered a Boss Fight, but I really haven't had much trouble beating even fully-operational Stations and I'd honestly like to see them get scarier and much less limited (I have had multiple runs where I can't even find a single Station, too; it'd be really nice if there were reasonable ways to get hints about where they are, like the Domain hints).