1)
Yeah, I've played two more hours after that and realized that. The problem is that I hit a massive wall after getting my mine like 15~ levels above the level when resources (carbon, copper ect.) are no longer required. It got extremely repetitive and slow vs. the pace of progress I had before and I was very far away from making a mega-structure. Then again, maybe I should've left the game to idle, because up to that point I was playing actively pretty much non-stop.
I've also read some more and seen how the late game advances. In general, it's going in the direction I'd like to see it go - you have to grab more planets to increase your income. The only problem (and obviously, this is because it's early in development) is that I don't see an interesting gameplay loop in just grabbing systems and building another gas giant miner. I feel like a part of the gameplay loop is missing here, where the player just isn't presented with enough interesting choices. Early game we get to play with all the toys and optimize our income, but later it seems like it'll get very samey. The best way to combat that, would be to automate a lot of the processes, such as having planet templates (or even system templates) and allowing the game to handle all the stuff you've been doing in the early game automatically, while letting you play with high-level stuff, such as choosing which systems to conquer/which enemies to fight ect.. Obviously there ought to be some pushback vs. the player, because as of now we're just derping around the galaxy and claiming rocks with no actual threats.
2)
This is kind of funny, because I'm actually also a developer (also in Godot) and I'm also making a strategy game. The economy present in Helixteus isn't that complex. If performance is the reason why you're using the collect all button, then that's not a good reason. In an optimally programmed game increasing income should not affect performance at all. Here's the solution:
Store a multiplier for each resource, example: technology for minerals and mineral upgrade for mineral gain speed.
Store a base income of each resource, modified only by buildings/megastructures similar stuff. Update that base income each time you upgrade/overclock/somehow modify a building.
Each tick (every second, half-second, w/e you decide) increase the resources by base income * multipliers * deltaTime. Because you overclock buildings, you also ought to sometimes check the overclock on every building - this is really slow, so you should do it rarely (no more often than every 5 seconds) and if you want a cleaner solution, instead of applying overclocks on buildings (which there can be thousands or even more of), change overclocks so they're more expensive, but instead apply to a type of building. So one overclock would boost all mineral production on the planet - way less clicks and waaaay more performant on scale.
With this implementation, you lose pretty much no functionality and can easily support worlds with millions (and more!) of buildings.
3)
Plateauing doesn't mean that things would go slower, you'd just adjust the cost of things. The purpose of this is to diversify the gameplay and change up the player's objective in the mid-game. Instead of increasing all your income by 20% with some technology, you'd instead have to shift your focus on conquering more planets. This would not only make things more interesting for the player, it'd make those technologies you get past the softcap (that maybe increase income by 1% each) far more rewarding, because of their scarcity. It'd also make the numbers more sane - if the player can see there's a difference of 100x between a level 1 mine and a mostly maxed out mine, then they'll be more easily able to understand the scale of things (it'd also make the game far more realistic, as everything eventually has diminishing returns, even technology). It's far more compelling to have a 1000 mines on different planets than 1 ubermine in your home system (I know this is only early game, but it's still a decently long part of the game).
4)
Oh, welp. I'm not sure if I missed some tutorial, but that would've helped a ton.
5)
Seems unusual balance-wise, but meh, jumps like that aren't inherently bad.
END)
I feel like your game has great potential, and I'll confidently say that you'd be able to sell it for $10-15 on Steam if the finished product has more mechanics (stuff that's engaging and challenges/gives options to the player) and decent polish. For that price tag though, you'd need to get some better graphics, especially in the UI department. As of now your focus seems a 100% on functionality, so I won't criticize too much, but the fact that my 2 month old project's UI that was created only for testing looks cleaner than yours means you should maybe look into it.
Don't undersell yourself, only because the game initially started out in flash. Even though objectively it's an unfinished mess as of now, it still kept me engaged for more than 3 hours. I'll repeat myself, but it has to be said - you have a great foundation. Looking over your discord and seeing you want to sell the game for 3 bucks made me wince - your game can worth far more if you put the required work into it. There are plenty of tools/techniques to make your game look far slicker.
Also a tip: don't feel boxed in the idle/incremental genre with stuff like infinite progression and prestiges. Your game could work great as a strategy with various minigames, or as some roguelike with unique runs. Pick mechanics that make the most enjoyable game.