This one line about the AWAKENING being before COVENANT, having come from this wonderfulguy's indecipherable language, is going to eat at me for years now. I'm gonna want that to end up as the title of the Prequel Novel, just so I can put it to rest!
As for the idea that the sequel may be a prequel, well, it may also be both? For instance, this movie starts before Prometheus, and then jumps ahead, right? So perhaps AWAKENING starts before COVENANT with SHAW and then jumps to the events after PROMETHEUS? This would involve both SHAW 'Awakening' on the Juggernaut with David, AND the COLONISTS 'Awakening' on the Covenant?
In fact, right now, my money is on that. This could also explain why the scenes with Shaw may have been cut from this.