1)
I believe you also missed that megastructures can be built way earlier than you thought: unlocking the mega-engineering science costs 100k SP and you can build Dyson spheres and mega mineral extractors right away if you choose the star/planet wisely (high luminosity-size ratio for stars, high atmospheric pressure for planets). I think this also gives the player interesting choices later in the game as some stars/planets have luminosity-size ratio/atmo pressure so terrible that it isn't even worth building anything there.
When you say "automate a lot of the processes, such as having planet templates", I think terraforming kinda already does that and allows you to transition from managing individual buildings to managing planets.
For threats, I don't plan to make this a strategy game, but rather a casual game where the player can expand without any stress, just a bit of thinking, clicking and time.
2)
Ah, right, sounds simple enough, I'll see what I can do. Fun fact: the Helixteus series was actually inspired by a Flash game called Bloons Monkey City, and I copied a few things including how you collect resources (click on farms individually to collect cash). Initially there was no collect all button, until people asked for it. And then it kinda stayed the same until now. I believe now's a good time for a change!
3)
I mostly agree, but "It's far more compelling to have a 1000 mines on different planets than 1 ubermine", wouldn't that make for very repetitive gameplay? One of the reasons to conquer new planets is not to fill them with buildings right away, but to look for interesting terrain features or planet properties (temperature, composition etc.)
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We're probably used to different things, but I personally find the graphics (that aren't placeholders) and UI to be okay and serve their purpose, except the settings menu, that one should really be cleaned up soon. I checked out the video you linked me, and I'm aware it's a test project, but it still gives me ideas for UI improvement, so thanks for that!
As for pricing, there are a few reasons behind the $3 price tag. I would rather see someone buy the game with low expectations and be pleasantly surprised than the other way round. This drives away people that go "$3 game? this must be crap", but I wouldn't want them to be playing my game anyways.
A second reason is that the source code is available publicly and the HTML5 version can be played for free, which will be identical to the Steam version without Steam cloud sync, achievements and high scores.
For those who really, really want to give more than $3, I'm also thinking of a ~$10 DLC of a pdf where I write the behind-the-scenes of Helixteus development, including screenshots of various ideas that never made it to the game or were removed. This does not put people without the DLC at a disadvantage while also offering the most supportive players something interesting to read and see.
Finally, a reminder that this started out as a passion project and it still is. I spent $0 making these 3 games, only thousands of hours of free time. I don't really view this as "selling a product", but finding those people who have similar interests as me.
I'll take a look at the other links you posted, they look really interesting!