My gripe with Deckard being a replicant is that it messes up two of the story's core principles:
First, that the Earth is so paranoid about replicants that killing them on sight in public is allowed without so much of a 'how do you do'. Doesn't make much sense to send another replicant to run around freely with a gun and a licence to kill. Futhermore, why would you build a world-weary, drinking, middle-aged, physically inferior gumshoe that feels pain to hunt superhumans?
Second, replicants can be identified because they can't produce subtle human emotions. In that regard, not only is Deckard very convincing, but he's also able to administer the Voight-Kampff test to Rachel, who is an experimental replicant that has implanted memories, something that is not even publicly known to exist.
Wow, getting into that subject made me look at a lot of things about the movie. By the way, what's the position on deleted scenes? Has the Movie Pope taken a stance on how they can be used to interpret canonical movie material?