Hi Ingix, again sorry for the delay - we somehow missed these comments until now.
1) Regarding the "Warm" level, as well as other levels, we are having a really hard time finding a good way to represent the input/output requirements in a way that is intuitive and readable. In the screenshot you attached, what is presented as the required output is correct - but imagine you filter out from the input every signal that isn't a warm color, and then collapse all the remaining empty (grey) signals - you would get the sequence orange, red - which is the beginning of the output sequence.
A general way to think about this problem is that there is no 1:1 match between an input signal in some location in the input sequence, and an output signal in the corresponding location in the output sequence.
In the input sequence, we show you exactly which signals the generator is going to create in each game beat. That means we have to include empty signals.
In the output sequence, however, we completely disregard empty signals. That is - if you can get your brains to produce the pattern "red empty empty empty red empty empty...", that would satisfy the requirements of an output "red red red...".
The reason for that is twofold - first of all, we can't know what the delay is going to be between the time the first signal is generated and the time it reaches the output sensor - that depends on the structure the player builds. Secondly, disregarding empty signals allows many more possible solutions to the puzzles, and some of them would be impossible without it.
Since the beginning of the project we knew that representing the input/required output in going to be a challenge, but we overestimated our ability to overcome it...
2) The numbers appear next to stages you've completed, and are a scoring system of sorts: the first number is the number of brains you didn't use in the stage, the second number is the number of brain connections you didn't use (i.e. the maximum number of connections possible between the amount of brains available in the stage minus the number of connections you used in your solution)
3,4) It's been a while since we worked on the game, thanks for the suggestions, we'll add them to the backlog, and if we get any idea on how to significantly improve the game which will motivate us to go back to it (for example, a solution to the problem described in 1)), we'll make sure to implement them.
Thanks again for taking the time to play and comment!