If you think about it, the biggest reason for doing this is preventing people from simply restoring to earlier after giving a unique pokemon to a friend or something (in other words, it would be too easy for everyone to get 150 without really having to give any Pokemon up)
I'm curious if EA looked at their stats more towards the end of beta weekend... on the last day, I definitely noticed half my matches were Rebel victories. On one hand, yeah, super easy for Imperials to maintain the edge in everything except the air, but Rebels can end the match with Orbital Strikes by second phase (hell, first phase if your team holds the objectives from the start).
TheApd_Returns' comments