probably because of the arbiter in league with the elites because he defected from the Covenant. possible reasonBecause Bungie still wanted you to fight them but was afraid the players would get confused on who was on their side and who was on the Loyalists side so only Elites would help you.
Following canon, it could be because the only Seperatist forces we see are Special Forces troops. Even while the Covenant was unified, the Spec Ops was primarily Elites (hence their title). Thus, this could mean that there still are Hunters and Grunts in the Seperatist fleets, but they are not sent to fight on the surface. Besides, Elites may have been expert ship commanders, but they were not skilled in maintenance. It's also possible that they ordered the Hunters and Grunts to serve as engineers and repairmen rather than soldiers.