Befor ending a mission, don't forget to sell all your buildings there. There is no penalyzation for selling your buildings; you just get the cash. Just don't sell your LZ. This often results in several extra transport loads of $$$. In the Recapture Nuclear Base ED mission, selling your used nuclear facilities scores you about 130,000 credits. This certainly will push your military a few steps forward.
Also, plan your research based on the deficiencies of your units. A better shield may be more practical than a stronger gun in some cases. You will need to build more units, but put research first. Ten extreme units will often perform better than 50 lighter, cheaper, simpler units. Just try to not lose your units, cannon fodder is not cheap.
ALSO; did anyone else feel like the last ED mission is kinda dumb? I always thought the last mission was supposed to be an all out war.