Damn! That was a good, and fun, and epic, and sometimes sad, trip. Yes, all of that.
SPOILERS ahead
When Lord Noriyuki told Tomoe and Usagi they had developped a second weapon to fight the invaders, I was thinking: "Please be a mecha. Please be a mecha. Please be a mecha."
And then, revelation: Usagi Gundam!
"Yesssssssssssss".

I am very fond of happy endings, so I was a bit saddened by the last death (even though it wasn't a complete surprise). I thought after all what they have been through all these years, Usagi and Tomoe deserved a shot at happiness in the end. But fate (and Mr Sakai) decided otherwise.
I find comfort in the fact that Space Usagi said it is not completely sure Usagi died this way, and records from medieval Japan are uncertain.
So I can imagine Usagi survived his last wound, but he has never been able to use swords again after that (which is why he passed them to Jotaro). He spent the remaining of his life as a councellor of lord Noriyuki and married Tomoe. Years later, when storytellers and bards wrote down Usagi's story for the generations to come, they decided a peaceful ending as a wounded samurai was not epic enough, so they invented this fantasy of Usagi dying in his last battle. And this is the story that was written down and survived for centuries.
Yes. That must be it.
