Except it's not about right and wrong, it's about what serves the story.
Nice try to make what I said about absolute "right or wrong" lol.
If they don't want to adapt a comic book character, I suggest creating an original IP. Otherwise it's a valid concern to try to keep to the source material as much as possible. It's a big part what makes these films fun to watch but difficult to make.
A better ending in my view would have been:
WALL OF TEXT ALERT!!!!!
having the robot suit samurai only the very beginning of that final battle. Wolverine eventually forces Yashida to abandon his suit out of honor and he emerges as a fully armored Silver Samurai with all the vigor of the young man Logan saved back at Nagasaki. The blade and armor he uses is made of adamantium so Wolvie's last remaining advantage is mitigated (I would have cut the awkward self surgery scene). An exhausted, near death Wolvie decides to die honorably and allows Yashida to stab through his heart. Unbeknownst to Yashida, this also dislodges and destroys the implanted parasite that was syphoning Logans healing power.
We see a proud Yashida walk toward another figure in the background who has been watching intently the entire time. We see him give his armor and the katana over to Kenuichio and says something to the effect of "I was wrong, mutants can possess honor. It is his legacy you must live up to now." Kenuichio bows deeply. As he comes up, he looks over to Wolverine's body but we see his eye's widen with fear. The body is gone!
Wolvie reappears behind Kenuichio and seemingly knocks him out. Yashida says something to the effect of "I am unarmed" to which Wolvie replies with a swift swipe of a claw "Almost", cleanly severing the man's right arm at the shoulder. Without Logan's healing power, Yashida begins to bleed to death on the floor.
A loud sonic boom erupts from behind Wolvie and he his flown several yards back. Kenuichio is now fully outfitted as the Silver Samurai with red hot blade extended out. Cutting back to Wolvie we see a massive slice on the front of his neck which has been cauterized from the heat of Kenuichio's katana which in turn
prevents the wound from closing up. Wolvie realizes this and frantically traces the wound with his claws a few times to allow his healing power to close it. Just as he recovers, Kenuichio cuts through his right shoulder in return for Yashida. Wolvie's adamantium skeleton stops the blow from severing the arm but the hot blade again cauterizes the surrounding nerves and tissue enough to render the arm useless.
Perhaps for the first time on film, Wolvie enters into a
true berserker rage. Singlehandedly he overpowers Kenuichio and knocks his katana completely out of the picture. He savagely reopens his shoulder before going in for the kill but the giant robot samurai falls between them. Yashida apparently had just enough energy to activate the suit's artificial intelligence. Wolvie pounces on the machine and proceeds to slice it down to the torso.
A countdown is activated on a panel inside the suit with a nuclear symbol next to it. Wolvie snaps out of his rage. They are deep underground after all the fighting where Yashida has also reinforced the structure to withstand a nuclear attack. He sees Kenuichio badly hurt some distance away, unable to flee the explosion in time. Wolvie goes over and kneels down next to Kenuichio "He told you to live up to my legacy..." and Wolvie covers him with his own body and a few large pieces of the robot as the bomb goes off.
In a split second, Kenuichio reveals a red hot katana and thrusts it through Wolvie's abdomen. Wolvie immediately recoils to expose Kenuichio to the full effects of the blast.
Logan emerges from the wreckage almost completely healed. The nuclear explosion was able to reopen most of the damage to his inner organs but he can still feel traces of the katana cut deep inside. His reflection in a piece of silver armor reveals a crop of gray hair around his temples and a few more lines around his face than he remembered having.
So another silver samurai emerges.
Thanks! 
