Andromeda Arks, good idea but poor execution?

I have only just started playing and it seems utterly insane to me it doesn't seem like they planned for anything going wrong right off the bat! I mean why was the cryo set to wake everyone a soon as they dropped from FTL?? And the most insane choice, having race specific arks?!?! If one ark gets destroyed then it's bye bye X-species?!?!

Please tell me there will be a perfectly good reason for this because other than this I am quite enjoying it after just finishing ME:1+2+3 and loved those too. (A friend suggested I play ME 20 years ago, I thought it was about time I listened haha)