Actually, they address this exactly in the Final Hours app. They felt an end boss would have been trite....I kind of agree.
Had they kept the one they intended to use, then yes I agree (they wanted to use the Illusive Man). The problem is exactly that in my opinion, The Illusive Man being the one they wanted to use to represent or to be the final boss.
They should have used Harbinger instead, there was enough foreshadowing about "him" in ME2. In fact, Harbinger controlled the Collectors, directed them to hire the Shadow Broker to find Shepard's body (Mass Effect: Redemption), so Harbinger had "interests" for Shepard, either his genetic material or "something else". By ME3's end it becomes clear enough that the ultimate goal for the Illusive Man was to control the Reapers, and if possible, to control Shepard, which he manages to do to some extent during the end (when Illusive Man "forces" Shepard to shoot at Anderson's gut). But beyond merely controlling Shepard the danger in Illusive Man was barely existent, since again at the end we learn from that SpaceBrat entity thing that he (Illusive Man) was already being controlled, which we all suspected at some point (that he was being indoctrinated, similarly to how Saren was, which is why via proper dialog branches you can provoke his suicide when he realizes that he was indoctrinated all that time).
So, BioWare wanted to use the Illusive Man as a final boss, even though they themselves knew that he was going to be armless if you managed to talk him down like we did against Saren. It would only be right after his "death" that his body would be taken control of (probably by Harbinger) and transformed into some Reaper-Illusive Man hybrid machine. That I agree would have sucked, or would have seemed predictable... BUT... it would have been better than what we current have in my opinion. With this said however I still think that a final confrontation against Harbinger itself would have been better, and of course I'm not referring to Shepard punching Harby's legs on Earth. I'm thinking about assigning War Assets at some point to fight against Harbinger, probably ending with the Normandy firing the long-calibrated Thanix cannon that happens to effectively pierce a Collector ship from one end to the other, which might have dealt a "final blow" against Harbinger, provided that the battle against him was able to weaken him down enough by using War Assets, such as Hammer team on the ground or Sword team ships firing at Harbinger from orbit.
In any case, having a final boss in the exact form that BioWare originally planned would have sucked overall. They still managed to come up with something worse though, I would have preferred that fight against a transformed Illusive Man over talking to that little kid entity thing. But as far as an actual boss goes I would have chosen Harbinger. And, as a side note, Harbinger's voice actor was used for ME3 (Keith Szarabajka), he voiced the dying Batarian at the Batarian refugee camp on the Citadel. They had Harbinger's voice actor and they didn't bother using him to voice a single line for Harbinger anywhere during the whole game's duration.
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