DEFCON document retrieval would work if maps were linear and with each advance over xeno territory marines could upload from a terminal or such, but that's not the case, and probably will never be, because that's not the type of game that CM is.
The collecting papers/files part honestly is flawed, not only because they're items which take space, but because if a marine dies with them in their pocket, they're basically gone. In my opinion, the whole system should work as a direct counter to mutators, by rewarding marines for killing xenos. After all, xenos only get stronger over time, so they should get strong as well. Give marines some hand scanners to scan dead xeno bodies and submit the data to ARES, perform some autopsies, whatever. Data retrieval could still exist, but it should be exclusive to terminal uploads and also guarded by xenos (or maybe map hazards?)