Actually, I think the biggest problem with its plot was that it sucked. The characters were bland, I didn't know their names because I didn't care, and I also didn't care when they died.
Why even have a plot if you're going to half-ass it like that? Really if they added around 20 more minutes of cutscenes they could have made it A material, but I guess they were concerned the countess five-year-olds that play Halo wouldn't be able to follow it.
Master Chief, the Arbiter, the Brute Cheiftain, the Prophet, Cortana, the monitor, Gravemind, and Sgt. Johnson were all well done, and I cared about them as characters. (I wanted to kill the Brute, Gravemind and Prophet).
But M$ wanted to cash in on the franchise without making too much effort on the inessentials.
What is happiness but the feeling of power increasing, and obstacles being overcome? -Nietzsche