I think the base game part is pretty good, although a bit slow.
Gophers&Galaxy is a bit crap/unengaging.
Right now augments seems completely pointless because any time spend on gathering and upgrading augments will disappear once you do a galaxy reset. Gophers should not reset on galaxy, and augments should be equipable and unequipable, which would make it worth spending time on upgrading them. That will fix the progression problem.
The galaxy upgrades aren't exciting or game changing in any way. There needs to be things like Autobuyer or unlocking new specialist trees etc. Something that will change the gameplay.
The contrast is really off putting, white text on light blue background isn't a good idea. Consider darkening the blue, or putting a black outline around the white text.
I think I know what is causing the crash/nan errors.
Something happens which makes the game not process (e.g. alt tab) then when the time skip happens, it goes back in time which makes some value negative, then negative time (or some other variable) doesn't make sense and that screws up everything.
This is a good game, well balanced in progression.
My suggestions to let completionists 'finish' the game:
One of the later things should award rubies every time (e.g. Final Quest always gives 1~3 rubies, endings give repeatable rubies).
For Quests it is too much clicking in the late game. Perhaps quests should auto-complete if you have already passed them (maybe with an option in the setting). Potentially you could also reorder the objectives to make incomplete ones at the top (that way there is still some work for the quests, but much less tedium moving the mouse around).
Something needs to be checked about enemy damage. e.g. allow you to upgrade hp, or reduce the range of monsters, or not increase enemy damage etc. Currently it is more of a luck thing to progress, especially since prestige is tied to maximum rounds.
Pretty good game, funnily everyone at the top end is cheating. Unfortunately I can cheat better than them.
If you want it to be competitive, some sort of limit of number of ships and levels would make it fair.
Is survival mode too hard (boring)? Just get the lightning gun, aim it at the flower in the center, put a weight on your left-click and come back in an hour.
To level up easily, grab xp, +speed/attack/agility/defense skills (in that order of importance), turn on as many modes as possible then rush their main building straight away.
Once you are high enough, every single level can be beaten by rushing their main building at the start, and if you want, nuking the building right before your troops land.
Really liked the battle system, the general feel of the game: "the detective", and "the librarian". I felt that characters with healing skills were a too powerful though, and the 'hard' difficulty, started quite hard, but got much easier.
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Oh... :( Has it resolved itself by chance? Send me a shout if not and I'll see if I can track it down.