Yeah, looking at it Defense is especially bad about that now. With exploration and science the limit at least increases as you get further into the game and it takes more points to convert. Defense does the opposite, starting low and potentially getting lower with certain upgrades. I'm going to change it to allow automatically breaking a charge back into points so they can be taken for the crisis system. I'd rather not add in a stage between playing planets and sending the points to their systems if I can help it as that would slow down the gameplay loop.
For the other systems I'll see if I can come up with something for them. Otherwise maybe I can do something with the crisis system to allow a kind of toggle-able magnet effect to send points there first or something.