In the case of having a final boss and how it would fit into the final sequences of ME3, Allow me to reference my favorite RPG, Chrono Trigger. The final boss was Lavos. First you fought the large outer shell that unleashed devastation across the world and is able to call upon the forces of across time to attack you. Putting the skills you learned in previous battles to the test. Defeating it is revealed that the creature was still alive. Going head first your crew goes into the shell and finds that Lavos body has been harvesting the essence of all life on earth since it arrived. It looks alien, it’s a torso that opens up to shoot lasers, arms that attack and keep the head protected. Only after destroying the arms is the head left vulnerable. Then after defeating that a strange creature is revealed with two floating orbs on each side. Lavos says nothing, yet your characters know that this is the final push but Lavos has a trick up its sleeve. Boss conventions say that the hulking Lavos creature in the center is the one to target yet after you kill it, the two floating orbs remain with one named the “Lavos Core” reviving the fallen creature and is much harder to kill than the rest. After figuring out the true heart of Lavos is one of the orbs, you take down its defenses and kill it. Time flashes before your eyes, you go back to your time period, there’s a festival, and your friends go back to the time period they are from.
Something similar could have been done with ME3. As Khayness mentioned, there could have been a huge ground battle. You lead your crew through the battlefield with reinforcements of the allies you’ve made while dodging attacks from Harbinger. Putting all those combat and leadership skills you learned to the test. After much struggle, you need help from the Normandy and the fleet engaged in the space battle to do any real damage, you did after all take out the Anti-Air cannons the Reapers had. So one of your squadmates and says, “Glad I brought this,” and throws you the targeting laser you used on Rannoch. So the Normandy succeeds in punching a hole in Harbinger, he falls but Shepard feeling this connection to Harbinger knowing it isn’t over yet. Boldly wanting to settle the score between them he takes his squad into Harbinger running into obstacles but reaching the core and destroying it. Then behind the core is Harbingers true form, something old, the size of a Geth Colossus, very machine like but with a sense of something organic. “Finally, we meet face to face Shepard.” After some dialog you realize that you have take him down, and in a similar way to Chrono Trigger you may focus your attention to the big center creature when there are these small floating devices that attack you and repair the center. (**And just for fun, you find out that the true catalyst is the “Heart of Harbinger” which is one of the floating devices.**) After you figure that out and defeat Harbinger’s true form (beaten and bloody) you make your way to the Crucible, attach “The Heart of Harbinger” to the control console and decide to either control or destroy the Reapers after talking with The Illusive Man. So how would this work out for a Final Boss? Good? Bad? Somewhere in between? Marauder Shield makes more sense?
In the end I think the merits of having a Final Boss far outweigh a decision to not have one because it’s too video gamey or cliché. And fighting with words comes nothing close to when your character says you failed to an enemy with a bullet instead.