The Last Battle + Secret Ending were poor
In my opinion.
Nobunaga in his Genma form was hardly much different than his form in Onimusha 2. He essentially had the same elemental attacks (minus his ice and earth from Onimusha 2). And all Samanosuke was able to do as a special attack was jump forward and slice. It got boring slashing away at those little orbs floating around him too. Very repetitive.
And as for the Secret Ending... yes Capcom that was well worth conquering the training levels for. Ako got enough screentime as it was. Samanosuke only had eyes for Kaede anyway, so why pointlessly include an ending of Ako trying to prove she could be 'all woman'?
The final battle & ending felt rushed to me.
Onimusha 3's a good game, but it's terribly overrated. Looked on favourably due to Jean Reno's presence (despite the travesty that is his English voice's absence) and the breathtaking opening CGI. Those two factors alone don't make a good game. The time travel plot was bollox too. They also missed Keita Amemiya as a character designer. IMDB & Wikipedia have him down as the character designer, but that's inaccurate. His official fansite tells me he is only mentioned in the credits for his work in Onimusha 2.
Onimusha 2 FTW!
PS.
Don't turn this into a Samanosuke vs. Jubei thread (you know who you are!).