You can't take the sky from me! (Plot) When MC and Cortana land on the deserted planet of Miranda Keyes, they discover that the Flood was actually created by ONI in an attempt to pacify the populace. Luckily, Cortana reveals heretofore unknown physical abilities and starts kicking Flood-ass left and right.
Mobile Cortana/Poorly realised Forerunner buildings (Location) Cortana is contained on a card that is seen for all of a few seconds in Halo, but in the film the card is slotted into everything.
Even if it's Forerunner technology and she can open doors, use the security systems, spy on Covenant forces using the security cameras etc.
Also Hollywood has a tendency to view all underground concrete buildings as nuclear missle bunkers. So the great and well thought out architecture of the Forerunners is replaced by contemporary concrete boxes and horribly uninspired low cielings and the odd security camera in the corner going;
*whiirrrr* *chk* *whiiirrr*
Either of those two things would seriously suck.
Ultimate Weapon (Plot) Some ultimate weapon or other that has spent years in developement for sole purpose of destroying the Covenant falls into enemy hands. MC is sent in to retrieve it, but realizes that he has no choice but to activate it immediately. Only then does he realize that the remote detonator or whatever is broken, and he (or another valued member of the cast, maybe one that was first introduced in the movie and is "expendable" as far as the Halo story goes) must sacrifice his life to make sure that the super weapon goes off.
Forerunners Revealed (Plot) There will be a scene in which this hologram comes up of a Forerunner after Master Chief saves the universe and he says "thank you for stopping the Flood." Then MC will take off his helmet and they will show his face, and he will get on a spaceship to another galaxy where the Forerunners are "alive."
Man of Few Words (Scenes) We know Master Chief is accustomed to using hand signals with his team (assuming we get to see any other Spartans). I'd be worried if they tried to play up the 'cool military angle' with a five minute scene of elaborate pantomime.
...Actually, that would make for a funny outtake.
Fake marine machismo/Elite zealotry (Characters) Instead of having lots of 'Oorahs!' and annoying macho cliches, make the Marines more like Saving Private Ryan. Don't simply tone it down; instead use it to show the horror of war and so on. Also, show how the Covenant are religous zealots e.g. scenen with Elites spouting religous stuff,or watching propaganda.
MC is a person too! (Plot) The thing that would ruin the movie for me: Humanity turns on Master Cheif for being different and exiles him. He valiantly defeats the Covenant while the rest of mankind is losing the battle and comes home victorious.
Halo must be Bourne (Scenes) Although slow "bullet-time" effects can look very cool at times, I think we can all agree that it would be completely out of place in the Halo movie. To address this Bourne Identity/Supremecy film ideas can be used. Having a good amount of action occuring in a small amount of time(4-5 seconds) can show the true ability of John and the other Spartans.
Get out da' big- Err, BIGGER guns! (Scenes) I hope they don't make it all ZOMGOWN3D big ol' guns to impress the idiots. Get into trouble, run out of ammo, swear, pick up the plasma pistol of a fallen grunt and try to survive till you can pick up a shotgun. How I play Halo, how Chief should play... Well... Life. Maybe a pack of Sangheili could get SPNKr'd a few times, but nothing huge.