Akainu destroying a government refugee vessel from the Ohara Buster Call in the name of "doing things right" is probably why he wasn't nominated. That wasn't some big war, and there were, clearly, other ways to make sure no scholar was on that ship, as opposed to blowing it up.

Because he's psycho. PSYCHO. He was killing foot soldiers that were afraid during the WB war. PSYCHO. What was even the point of that? He was just wasting time doing that!

So in the eyes of anyone, would you say that this person was fit to lead all of the marines? No matter what his "results" were in battle, the event at Ohara was pretty heavy foreshadowing at what type of character Akainu is.