So I feel like a lot change since I played it last, the biggest change being, before when I click on the cubes, they would burst and explode nearly right away in groups like chain explosions. Now it has changed to where I need to constantly click on the one cube to get it to explode, which is fine, and I can see this is obvious as the cube (large dust) becomes increasingly red over the number of clicks. I feel like you changed the mouse click radius or the area of effect that influenced the logic that breaks the cubes apart. Which I get a sense you did this to slow the pace of breaking apart the dust into fragments and increase the impact that upgrades have on different behavior / mechanics.
I had not experienced the upgrade system up until now, so I am not sure what kinds of issues other people were having (the payments possibly too expensive). I believe this upgrade system will be a huge balancing act. As this is my first time having access to it I am finding that I receive such an allowance of spendable points that I burn through the upgrades extremely quickly without fully grasping impactful changes that influence the gameplay in a gradual way. The upgrades escalate very quickly, drastically changing the gameplay, especially as you get to wave 4. I am not sure what your are expecting for an average target time of 10 runs was to be, but I did it within a few minutes.
I also noticed that the dust particles were producing so fast and being absorbed much more quickly this time around instead of whimsically swirling around in a orbit where the gravity increased over time, pulling them in like a whirlpool. I personally did not get to enjoy the visual effects of the dust particles and their trails the same way I did the first time I played. They are being absorbed too fast into the core. I liked taking in the detail of the particles winding in. This effect is even more so after i maxxed out some upgrades that influenced the rate at which the dust gets absorbed. While yes you had some dramatic screen shake last time around, I think you should consider adding it back, but only so slightly. I feel like in general, the screen shake was crucial to convey the sense of energy and power that cosmic forces would be perceived to have, it fed into the theme of the project. Or at least make it an option to turn off, but either way, I thought the screen shake was meaningful, just needed to be toned down, or even just added to the part where you are clicking on the core to expand it. (because now it doesn't feel present at all~ which for me lessened the visual feedback and entertainment value).
I noticed that I was still able to collect dust particles after the time was up, adding to my mass (even after the core was ready to level up). So after the seconds were done I could just keep collecting the rest of what was still floating around, adding to my mass as spendable allowance (not sure if this was intentional).
I feel like you should really change the green text from that bright yellow in the Upgrade UI. The green text can burn your eyes out, I found it really painful to see (personally). Then when it change to black text, I was like "oh freakin thank you lord" XD. I would consider the black text as the staple state for readability against the yellow. I would also say you should apply desaturated values to the UI. Like how you have those side bars Strange/Anomaly/Fragment~ those are so readable and easy on the eyes. Or even the same color scheme you used on the Start Menu is more readable and easier on the eyes. That yellow is so bright and when you pair it with another bright color, its too much... but if you dropped that yellow saturation (if yellow is the color you are trying to design with), it would feel much better. And partly because the yellow buttons takes up about 40- 50% of the screen space. Booom! Then I hit that last level with the Yellow screeeenn looll! Noooo!! XD
https://color.adobe.com/create/color-contrast-analyzer
This is a really useful tool in general for colors if you would be interested in any trial and error experimentation for color choices.