The problem was that Blizzard couldn't just flip a switch to randomize the battleground's spawn points: they were hard-coded into the moving ships that players appear on, so it took much more coding to use a coin-flip start. However Zarhym now confirms that the coin flip is coming to SotA. And though he didn't say when in the original post, the Patch 3.2 notes tell us that it's coming in that patch.
Hopefully Blizzard will have learned their lesson for the Isle of Conquest -- although since it's closer to Alterac Valley from what we've heard, we probably won't have that asymmetrical issue, and both sides will be able to start with just as many advantages and disadvantages as the other.
Patch 3.2 will bring about a new 5, 10, and 25 man instance to WoW, and usher in a new 40-man battleground called the Isle of Conquest. WoW.com will have you covered every step of the way, from extensive PTR coverage through the official live release. Check out WoW.com's Guide to Patch 3.2 for all the latest!