I've reached the endgame of this game: Infinity of research points without going out the starting planet in a new universe.
I was playing offline version v0.21.1 . I haven't played higher versions yet, but most of these problems probably still exist.
I've encountered a few problems:
1. Megastructure stage: Terraforming planets for Atom Manipulators or Subatomic Reactors cost way more energy than they should
Normally terraforming planets for a specfic building is equivalent to have X buildings of that level, without any bonus from CBDs. X is the surface area of the planet.
For these two buildings, terraforming for them not only increases the speed of processing by X, but also increases the energy cost by X. X is usually very large, around 10M or even higher. This makes terraforming for these two buildings unusable, as the energy cost is prohibitively high, even with late game megastructures. Even refining stone becomes difficult with 10Mx energy cost.
If you build X of them instead, you will process X times faster than a single building, while consuming the same amount of energy for the same amount of material. If you do put X times more materials into them, you will spend X times more energy.
2. Dimensional stage: Infinite research multiplier way too OP
In my savefile, I increased this factor to 6. This is immensely OP, as I could reach infinity research points on my starting planet, with just 1 miner, 1 storage, 1 generator and 1 lab, all upgraded to very high levels. These buildings are level 1100, and the lab infinite research is level 369. At this level, the buildings cost ~1e130 creds. This makes my lab go over 1.8e308, and creates several NaN issues LOL
While the infinite research itself alone won't break the game, it multiplies with building levels and CBD bonuses, which does break the game.
3. Also dimensional stage: Probe points and Dimensional Remnants
According to the release notes, this seems to be nerfed, so might no longer grow broken.