I've been loving the game - a really great incremental (and I have played a lot of incremental)! I do like that the game unfolds layers as you go, and I love it when an incremental game does that. I also appreciate that you have a meaningful prestige system... which turns into a basic and automated mechanic later on.
I was even enjoying that Stage 5 (which a lot of folk don't seem to like), and I like that it was not just a complete cakewalk...
...but it seems like it can be a bit too challenging at times, and that there are unwinnable scenarios that can happen - or if there's a mechanic to win, it's not clear.
I'm currently stuck on The Screaming Maw; on other maps if you revealed too much of the map it could increase the challenge because more things would infect your stuff - but on The Screaming Maw, I seem to repeatedly get soft-locked because constant pys-screams from multiple different screamers. And they all seem to have the crystalline-super-defense on them, even if they aren't anywhere near a crystal, making it a real slog to shoot them down.
I suspect that some folk aren't articulating their issues with Stage 5 all that well - but I think a part of it might be that it feels like it's disconnected from the main idle game, and that it is a bit of a bait-and-switch. For example, Stage 5 can require a lot of focus and precision timing... which is kind of the opposite of the idle game folk had been playing up until that point. So I think that's part of the grievance that folk have.
As for my greviences with Stage 5 - well - I have some usability suggestions that I think will help without taking anything away for those that like it how it is. First off - being able to destroy and build while paused would help *a lot* (presumably, a built thing would just be stuck at 0% until unpaused). It would mean that folk like myself who have hand problems and/or limited dexterity could still play this part of the game. And it doesn't hurt people who want to play without pausing - they can still do that.
My other thought is that maybe Stage 5 doesn't have to be fully disconnected from the main game? I think folk may like being able to leverage their idle economy and that'd help connect Stage 5 to the first four stages.
For example - perhaps I can spend a few million Pristine Light to give me some sort of edge or advantage in the realm-fight-RTS - and using these advantages would be entirely optional.
Perhaps some of the impassible terrain could be destroyed with a Pristine Light Bomb, to open up more options and routes to victory. Maybe I could super-charge a Pylon to extend it's range, or perhaps I could power-up a pylon to also destroy dissonance - etc, etc.
You can even make it clear that it's an optional extra that isn't necessary and only for folk who want more options in the RTS; heck - feel free to have an achievement for clearing the post-clear simulations without using these reinforcement options.
I think that'd help folk that are frustrated with the difficulty, folk who have accessibility needs, and folk that wanted more of an idle game.
If someone wants to blow 100 million light on a level because they want to steam-roll it because that feels more idle-game like? Let them.
There's no pleasing everyone, but, adding options - even calling them 'idler options' or 'accessibility options' at least let folk who are invested actually see your game through.
I hope my thoughts are helpful.
Keep up the good work!