Wait, you're complaining about inconsistent characterisation? You have a The Stolen Earth/Journey's End
. The blockbuster story where seemingly all the normal, everyman characters randomly came back as soldiers wielding huge guns (Rose, Martha, Mickey, Jackie). Doesn't get more insanely inconsistent than that.
Lindelof is a good writer with some impressive Lost episodes under his belt, I don't blame him for Star Trek Into Darkness. I do kinda blame him for a lot of the flaws in Prometheus though that script went through 5 billion drafts so it was always gonna be messy.