Possible consequentialist response: our instincts are inconsistent: i.e., our instinctive preferences are intransitive, not subject to independence of irrelevant alternatives, and pretty much don't obey any "nice" property you might ask for. So trying to ground one's ethics entirely in moral instinct is doomed to failure.
There's a good analogy here to behavioral economics vs. utility maximization theory. For much the same reason that people who accept gambles based on their intuitions become money pumps (see: the entire field of behavioral economics), people who do ethics entirely based on moral intuitions become "morality pumps". If you want to not be a morality pump, you essentially have to choose some situations in which you go against your moral instincts. Just as behavioral economics is a good descriptive theory but a poor normative theory of choice under uncertainty, deontology is a good descriptive theory of human moral instincts, but a poor normative theory.
Cf. Joshua Greene's research in moral psychology and the cognitive differences between "characteristically deontologist" and "characteristically consequentialist" judgments. Previously discussed on Less Wrong here.
For much the same reason that people who accept gambles based on their intuitions become money pumps (see: the entire field of behavioral economics), people who do ethics entirely based on moral intuitions become "morality pumps".
I think this thought is worth pursuing in more concrete detail. If I prefer certainly saving 400 people to .8 chance of saving 500 people, and prefer .2 chance of killing 500 people to certainly killing 100 people, what crazy things can a competing agent get me to endorse? Can you get me to something that would be obviously wrong even deontologically, in the same way that losing all my money is obviously bad even behavioral-economically?
My apologies if this doesn't deserve a Discussion post, but if this hasn't been addresed anywhere than it's clearly an important issue.
There have been many defences of consequentialism against deontology, including quite a few on this site. What I haven't seen, however, is any demonstration of how deontology is incompatible with the ideas in Elizier's Metaethics sequence- as far as I can tell, a deontologist could agree with just about everything in the Sequences.
Said deontologist would argue that, to the extent a human universial morality can exist through generalised moral instincts, said instincts tend to be deontological (as supported through scientific studies- a study of the trolley dilemna v.s the 'fat man' variant showed that people would divert the trolley but not push the fat man). This would be their argument against the consequentialist, who they could accuse of wanting a consequentialist system and ignoring the moral instincts at the basis of their own speculations.
I'm not completely sure about this, but figure it an important enough misunderstanding if I indeed misunderstood to deserve clearing up.