While you can't deny the 'cool factor' of fighting the beautiful but deadly Covenant ships, at the core it's the same old tale: humans fighting aliens. The Halo universe does an excellent job of expanding the different races of the Covenant, giving them motives and culture. However, the human vs human conflicts have a the capacity to go much deeper. Civil war, civil unrest (especially in today's world; have you seen the Middle East lately?) and combat amongst ourselves goes back to the beginnings of humanity. We can much more easily understand the minds of other humans than we ever could an alien species. Also, the rebel factions in the Haloverse act much more deviously and less overt. When the Covenant attacks you have a very clear-cut goal of taking down their ships or perishing. Fighting rebels, it isn't just kill or be killed; there is room for negotiation and a chance to minimize the loss of life. That adds a whole world of complexity to the struggle.