One of the most recognizable franchises of all time, the Halo series provides some possibilities of possible matchups and story ideas with other franchises.
* Xytan 'Jar Wattinree vs. Thrawn= Both are highly regarded as deeply respected fleet commanders in their universes. Brilliant tacticians, only their personalities separate them from each other in differences. (If you want to know about Xytan, here's the link: https://m.youtube.com/watch?v=9atnLD5HpAs) If there was a deciding factor in who would win this match up, Thrawn would have the advantage in this fight in regards of him learning and understanding a species culture and studying his enemy tactics. But the final outcome would be uncertain: would both naval geniuses come to a mutual agreement or would it be more of a fight to the death!
*The Covenant vs Apokolips: Lord Darkseid is known no better than an unstoppable force bent on bending other planets to his whim. If he encountered The Covenant, would they just be another collective of insignificants to have bend the knee to him or would they have a chance against Darkseid and his forces? Ultimately I would say the win would go to Darkseid.
The Covenant vs Thanos: The same idea as above but Thanos is a death mongering villain of the Marvel universe. Though personally the Infinity Gauntlet would be the one trump card in this fight unless the principle of the gauntlet working in its own universe applies in translation.
Spartans/Elites vs Predator(s): The ultimate hunters hunt the best warriors from both sides of the Halo universe. In my personal opinion, the Elites would have the slight edge in terms of weaponry as the Spartans would have experience in fighting cloaked enemies. Or to make it more interesting, both elite teams from each side would work together to best a team of Predators.
Aliens vs the Flood: both are among the most dangerous alien species in science fiction. Only makes sense to have them clash against each other. Both are known for acquiring new hosts and working through a hive mind. Even when the Xenomorphs may have acid blood as their ace in the hole, I'm not positive if they would possibly find new hosts in Halos' parasites as it be contrary to that of the Flood. Aside from a better chance of acquiring a new host, the Gravemind may possibly have a better capability of handling the Alien queen.