Hmm, could you be more specific? I recall fixing a few bugs and tweaking faction weapon availability (in particular, iirc, giving pirates more stuff so that their high-tech stations aren't so sad) but I'm not aware of any particular issues with autofit. Perhaps some of this is a difference in expectations? It's not supposed to produce highly optimized best-in-class variants; rather it's "generally a mix of halfway-reasonable stuff, with some variants that are fairly random". It does get more consistent/produce "better" outcome as fleet "quality" goes up, though... anyway, any more feedback here would be very much appreciated!
There is perhaps quite a bit of difference in expectation. Many of us are still living with the memory of DynaSector and the incredibly dangerous and absurd fits it provided.
Now that said the current iteration of autofit does some... very silly and incredibly dumb things quite often. Like giving ships weapons they can't use effectively at all, such as giving slow ships short range weapons or downsizing mounts in ways that don't make sense (such as the larges on a Conquest).
It's basically to the point that often enough AI fleets simply aren't a threat because their loadouts don't work, or are only threatening because they have weight of numbers. I understand that you don't exactly plan to tune autofit to the point that it's always incredibly dangerous and daunting to even consider combat, but it really does need some fine tuning to give the AI more of a fighting chance.
Downsizing by autofit in any way is almost bound to be a mistake.
I appreciate the added detail! I guess in my mind, "autofit" and "what the default fleet inflater tells autofit is available to use" are two different things, but it makes sense that it's not... a very player-facing distinction. I'll take another look; pretty much all cases of downsizing for example (or using a short range weapon when the base loadout uses a long-range one) is due to nothing better being flagged as available. I've made some notes and will take a look shortly.
When can we expect a .95a realease? :O
When it's ready, of course

The size 6 planet limit seems to be pretty fair all around. It really takes too much game time to hit 8 or try going beyond that in an ordinary game. Still, it might be nice for various planet properties to increase or decrease that limit. Your average crappy post collapse colony might be a 6, but a neutron star might cripple it down to a 5. A super nice highly habitable gaia world can be a 7, and maybe a super rare planet terraforming tool could push it up to an 8? At that point the world would practically be the New Earth of the sector. In any event it would take real extreme circumstances to change a planet's limit, so it'd be the exception rather than the norm.
Hmm. I could see perhaps hazard rating changing the size limit - but then there are some ways to manipulate the hazard rating now, so I think the "soft" natural limit (based on growth penalties from hazard, but over-comeable via hazard pay) might be an easier fit.
Since the colony changes keep coming up, as well as the core planets being too much of a pushover, i just wondered if you think they become more resilient or less with all the changes? ... What about adding or upgrading their defences that aren't linked to colony size (like orbital and ground defences)?
I think they're in about the same place. Just in general, I'm not particularly concerned about this aspect of things. The core worlds need to be reasonably vulnerable to things like sneaking around, smuggling, raids, and so on; that's more important imo than their overall reslience/power level vs endgame fleets. It's not like taking them down is any sort of goal (other than self-imposed), and they're not the toughest challenge in the game anyway, so it's just... not something that I think will matter very much in the long run, not when there will at some point be a "proper" endgame to focus on. And based on the requirements of that, they may end up getting tuned up or down defense/power-wise! But right now, there's nothing actually meaningful to balance them around, if that makes sense.
And are you filling up the extra colony slots that open up on various AI planets under the new rules? (and if so did you manually adjust total market values or did they "just" automatically increase a bit?)
Definitely not! Just a few items here and there where they were absolutely needed to make the default economy's ends meet. I'd like to keep as many of the items as possible a fun surprise, not, "oh, it's that thing I already saw on some core colony".