In so far as badges are concerned, if they are implimented in such a way that they grant tangible benefits, it should be up to the player (PHALANX commander) to decide how to distribute them. This level of control would be balanced by the limited availability and quantity of the badges.
That all said, I would like to see some sort of training facility with or without a limited capacity. Each soldier utilizing the facility would train in a number of player selected areas, causing the selected skills to advance slowly over time while the soldier remains at base. The fewer skills selected for training and enhancement with respect to an individual soldier, the faster those selected skills would develop for that soldier (total skill points/experience gained is diffused between the total number of selected skills). Of course, any skill advancement gained during in-base training is identical to skill advancement gained through missions for the purpose of calculating the difficulty of further development. Further, skill advancement via in-base training is subject to the same restrictions and limitations of skill advancement through missions.