First impression: A really well polished game with lots of neat little details. But some things that need attention.

A definite fan of the UI. Everything is clear and easy to find.
Soundtrack is really nice, but could use a little more variety.
Very impressed with all the dialogue and advisor fluff. There's a lot of effort gone into this and it shows.

Building transports and assigning them to the trade pool constantly is a bit of a chore.
It would be nice if there could be a setting specified colony-by-colony that would automatically pause whatever its doing to build and assign transports to the pool whenever new routes open up.
And returning to its previous task once all routes are covered.

I've been a bit frustrated that I haven't had the opportunity to really use a lot of the unlockable items because by the time I'm in a position to use them they're already obsolete, and I've moved on to something better.
(This is not a problem specific to SiS. Many such games have a similar issue.)
Is there any way of slowing down technology progress, like a global setting or other user definable constant?
If there isn't, could there be?

When viewing the individual race info, it would be nice if it were to display a list of all the habitation types in order of preference for that race.

Terraforming is a little odd sometimes. There does not appear to be any rhyme or reason (or I'm missing it completely) as to which planets are able to be terraformed at all.
This could do with giving the player some (more obvious) feedback as to the limits etc.

Also, when presented with the various options for terraforming, the tooltip only displays the preference of whatever race the player empire is. This allows the player to make some very damaging non-reversible choices by terraforming a planet to a type unsuited for its current population.
Suggest re-working this to display either:
- the preferences of the dominant race on the planet
or
- an ordered list of races who would prefer that specific change

Some terraforming tech is described backwards from what it should be doing.
Orbital mirrors are described as something that improves conditions on a hot planet. But mirrors would only make conditions worse by adding more solar radiation to the planet.
Mirrors would be used to warm up cold planets.
Hot planets would be cooled by orbital shades which block the path to the local star and reduce the incoming radiation recieved.

The fleet combat UI works well for small scale battles. But falls apart when there are multiple dozen ships on the player side.
When the player fleet is large it is incredibly easy to miss out ships as there is no indication of which ships still have actions left and which don't. Nor is there any (obvious) means of cycling through all available ships.

Initial starting formation for fleets are not ideal.
Usually you'd want heavy armoured units front & centre, support units behind, and fast units on the flanks.
But SiS arranges them with small units front & centre, heavies scattered throughout, and supports on the flanks, which curve toward the enemy like a pair of claws often putting them far in front of the centre ships.
Every large battle first involves pulling back these support units and advancing the heavies, which is incredibly tedious.
This especially badly impacts the Orthin who can field dedicated light artillery, which being small are placed on the front line. Where they die in droves on the first enemy turn. These "gunships" should be as far back as possible.
This really needs some attention and/or the ability for the player to define custom start formations.

Viscids. Why? Why are these things in the game at all?
They have no purpose whatsoever, except seemingly to frustrate the player.
The only way I can think of to get rid of them is to build transports, load them up, and scrap them. Which is sadly impossible to them having the "sessile" trait which means they cannot be loaded into transports. Ugh.
Please consider doing one of three things with them:
- re-working them into being useful in some way so that the player will want to keep, or at least tolerate them
- giving the player some push button option that "removes" them from the colony for some kind of cost
- removing them from the game entirely

Are Humans supposed to be terrible neighbours?
I always end up at war with them because I won't just give them colonies. They don't seem to "get" that this is not a happening thing without some serious incentive. But they offer nothing and will constantly barrage you with these "requests" until they are angry enough to go to war.

Overall impression: Uncut gem. Impressive, but needs some work to truly shine.

[e]
Just digging through the files, and found a ton of solar radiation and mechanics stuff buried in the system gen.
<3

[e2]
An example of an odd terraforming choice with no good outcome:
i.imgur.com/7ikJNhy.png
A small ocean world with a roughly 50:50 split between Human and Phidi.
Both terraforming options are a marginal improvement for Humans, but hugely detrimental to Phidi. So a net loss overall as I'd have 2 less population either way.
I'm playing as Humans, so the tooltips only mention Human preferences. Which in this case is not really helpful.
I tried both terraforming options and it offered no further improvments, even with maximum tech. So this is essentially a trap choice.

Also just noticed that colonised planets have different nightside illuminations for terrestrial/aquatic species, which is a super-nice detail.

Had fleet deployment with civilian ships, which were on the flanks further forward than my front line!
This is most uncool.

And the Phidi are colossal hypocrites. :P
Give me a diplomacy penalty for being at war, but also ask me to declare war on someone else AND break treaties in order to do so.
Away with you perfidious fish!

Nice, thoughtful observations!

One thing that seems odd to me: terraforming does give a warning when it will be detrimental to other "secondary" species on the planet. This happens, in the planet menu, when choosing the terraforming option - something to the effect that "this will improve your species' habitability to blahblah, but will reduce the population limit for others to suchandsuch.

Or does that only come up when the current size is greater than the resulting maximum for the other species? I didn't think so, but I admit I'm going from memory.

The terrafoming tooltip states:

'Terraforming <PLANET_NAME> to a %s would decrease the population cap from %d to %d. However, our %s colonists would prefer the new environment.'

(\LUAstate\orders\terraforming.lua)

The oddity being that this is displayed even if there are no human colonists on the planet, and in many cases the new number is worse than the existing.
This is the same for every player empire, the tooltips only ever display the preferences for whatever the empire race is.

So far as I can tell, small planets can't ever be terraformed further than arid or glacier. So if you have aquatic population on a small ocean world, you're probably ignoring terraforming there forever.
(Thin atmoshere restriction maybe? Sensible, but still needs feeding back to the player.)
Warm planets medium size or larger can be terraformed fully.
Cold planets don't seem to have any options at all.

Generally, at every step you have to check the tooltip. And if at any point terraforming results in a loss of population capacity, it stops where it is because more population = more output.

Another observation is with the ship designer.
It would be really nice if there was some way of reducing the amount of scrolling involved once you have accumulated a wide range of equipable items.
This could be separate lists for weapons and equipment and/or the automatic pruning/hiding of 'obsolete' tech.
The ability to double-click items on the list to install them would be nice, but would also be a non-trivial exercise for weapon placement.

Also, the designer really needs some way of showing the player if certain weapon mounts have restricted firing arcs.
Some are obvious. But others are less so, and I only know about them due to putting PD weapons in a slot and being disappointed by not being able to use them properly.
Again, a feedback issue.

[e]
Playing as Tinkers is hard work. Their pops have horrible research and economy output, which means that ironically they can't afford to harmonise population because they really need the boost from them.
Even though they have a huge industrial output, they can't really afford to use it unitl well into mid/late game as they need planets focusing on trade & research to just keep up. Especially when exapansion options are limited.

Thanks for the feedback.

We are in the process of completely reworking the terraforming system for the next expansion. The current system was kind of an afterthought, endgame toy. The newer system will allow more incremental terraforming changes earlier in the game.

The Viscid are a negative characteristic to a planet, in the same vein as metal scarcity or adverse environment. We have some ideas to make them perhaps more interesting as a gameplay element, as people do seem to complain about them in a way they never seem to complain about other planetary drawbacks.