For the generators, I believed this issue was fixed in v2.61 however I've since reworked the max-buy calculation to be better. Hopefully in the next update this is no longer an issue if it's still present!
For the upgrades, I've thought that same but haven't decided what I'd like to do (if anything) regarding this. The talents for these is more so meant as a means of not needing to keep upgrading them, seeing as they have a cap. Where as increases to damage and other similar stats you'd want to scale forever.
Click speed is meant to be maxed out relatively early simply because people will just use an auto-clicker so I may as well add it to the game. We don't need to be getting RSI!
Cube size and cursor radius I've been wondering about moving them away from upgrades and being instead tied to something else, maybe only as talents or instead tied to stage level but would require me to re-balance everything. I'd love to know what people think, if that'd be any better or instead keep the current system and just have me adjust costs.