The concept of performance being a collaborative process is not unique to motion capture roles: ultimately any on-screen performance is shaped by the director, the editor, the cinematographer, the make-up department, the costume department, and many more members of the production and post-production crew. In an action movie like Dawn of the Planet of the Apes, Serkis isn't alone in being absent from his character's actions; for example, human lead Jason Clarke had multiple stunt doubles.
From an outsider's perspective, it's honestly difficult to gauge the ratio of actor-to-animator input that ends up in the final cut of a film. Twentieth Century Fox has released featurettes showing side-by-side comparisons of actors and their ape counterparts, reflecting Serkis, Letteri and Reeves' statements that animators try to translate the original performance as closely as possible. These snippets only represent a tiny fraction of the film's total running time, however, and skeptics will be able to claim they have been cherry-picked.
One of the main problems with the whole controversy is that the charge against Serkis has been led by animators who don't work for Weta, and claim offense on behalf of the people who do. Serkis, Reeves and Letteri have all indicated that Weta now has a very unique, very specific approach geared towards honoring the actors as much as possible. If that's the case, then it's possible Weta's visual effects team might actually concur with Serkis' statement.
Without hearing from those people at the heart of the process, this conversation is missing a very important voice. Screen Rant tried reaching out to some of the Weta crew that worked on Dawn of the Planet of the Apes in order to get their perspective on the issue, but it quickly became clear that the team's hands are tied by strict NDAs, preventing them from speaking in detail about the processes that they use. One Weta animator did tell us, however, that "in the end... the final motions of the character are the way they are because of the director, not Andy Serkis or the animators."
With awards categories now struggling to keep up with the pace of filmmaking technology, the question of who most deserves to be on the stage to collect an Oscar for a motion capture performance remains a difficult one. At the end of the day, however, the amount of available space behind the podium isn't exactly limited. You could probably fit more than one person on the stage.
Of course, the entire debate may prove moot given the Academy's overall reluctance to honor science fiction movies (or other genre films) outside of technical categories. Rise of the Planet of the Apes only received one nomination out of the 2012 Academy Awards for Best Achievement in Visual Effects (the win went to Martin Scorsese's Hugo).
For anyone who feels troubled by the way that actors are thrust into the spotlight while crew are left in the shadows, you can at least take comfort in the fact that, for now, the animators behind the Apes movies have actually received more Oscar recognition than Andy Serkis ever has.
Dawn of the Planet of the Apes is out in theaters now.