@3Dandbeyond
Yeah.
You know my stand on IT. I don't subscribe to it, but, it is the "easy" way out for Bioware. Personally I'd prefer a ME2 style, assign your squadmates key areas and making those choices matter.
In regards to the boss fight, there is a way to make the Crucible make sense of sorts. Let it be a transmitter that allows you to "hack" into the Reaper's AI VR world, very much like on Rannoch with Legion and the Geth. The Catalyst, a living mind, in this case Shepard.
Allow ONE other person to go with you, and depending on if its your LI or not, have that person play a huge role in you making out alive, there will be a "cost" attached of course, and I already can think of a few, much like in Babylon 5, both or one will have his / her life shortened.
So, this last fight, will be a two man party fight against a VR representation of Harbinger and the rest of the Reapers consciousness, programming, hive-mind...whatever. It already has a precedence on Rannoch, and it doesn't "bend" the rules too much, and you don't have the "improbable" issue of Shepard fighting Harbinger with a peashooter Blackwidow.
Plus, it'll give the writers leeway to "disable" Reaper systems thus allow the Alliance Fleet to win a conventional fight against the reapers.
Shepard lives, but will suffer some form of trauma. (what I already have in mind is for Liara, since She seems to be the canon LI) that will not make this a "free ticket" and will tie up nicely with her Shadowbroker issues and her and Shepard being Married. (I hope you didn't think she can still be the shadowbroker and have a kid and deal with marriage,

)
Anyways, just a thought.
More fanfiction material since Bioware doesn't care.