Well, an innate capacity would imply that most people would be quite good at evaluating simple logical syllogisms and if/then conditionals. Yet, research shows that people are generally quite poor at deductive logic, with the majority of people getting some simple logic problems wrong. This is true if you give people abstract forms of arguments (If p, then q; Not q; therefore not p). Most people will incorrectly say this conclusion necessarily follows the premises and/or will generate that conclusion from the premises. People get better at it if you use real world concepts and relations in place of abstract tokens, but that only demonstrates that people are not using deductive logic to reason about the problems. Also, if you use real world content, people will be even worse if the logical validity of the conclusion contradicts their a priori beliefs about the conclusion. IOW, people generally cannot apply logical reasoning to arguments independent of their a priori agreement with the conclusion.
Of course, some people are better at logical reasoning than others, and that is partly predicted by measures of general cognitive ability but also by measures of thinking dispositions where some people are more prone to go with their "intuitions" and prior beliefs (aka biases) and others are more able to set their beliefs aside and evaluate what is implied by a set of given claims. The difference between ability and style is the difference between what one can do if they try versus what one is inclined to try to do.
In fact, more religiosity predicts greater logical errors due to a tendency toward a more intuitive less analytical cognitive style.
I agree generally that most people are not very good at formal reasoning. However, most people are not very good at singing from a score either, yet most people can learn to sing. Most people are not very good at writing and reading, yet most people can talk and understand other people talking and most people can learn to read and write. I think any research on our logical capabilities would need to make that distinction.
By inherent capacity, I mean a natural capacity. We all display this capacity each time we understand what people mean from what they say. Our brain is wired to use rules and using any rule correctly is a logical capacity. We need first to learn the rules themselves, or rather our brain needs first to integrate the rule in its processing of the information but this is the result of learning. Definitions are rules. Learn a new word, say "diorite", and from this point you'll understand what anyone using this word will mean with it, or at least assume that's what he means. People can't speak a language unless they somehow learn it but I think we would all agree we have a natural linguistic capacity, whether it is derived from a more general capacity I don't know but we have that capacity. We all learn a language but we don't all learn formal logic, and indeed very few people do. Formal logic itself is just one of the many things we can do that require a logical capacity. Think of even being a racist. Being racist is basically having somehow memorised a rule saying all people of that ethnic group are cheats or murderer or whatever and then going on to apply this rule to any fellow of that ethnic group. Same for sexism and any discrimination. So, even being an idiot requires a logical capacity.
I would also agree that most people don't use formal logic to reason but that's really only because most people don't reason at all. Ask people why they do stuff and you'll see what I mean. Indeed, most of what we do we do it without reasoning about it first. We just do it. Reasoning is for "intellectuals". Indeed, most people dislike people who argue their views. But even intellectuals don't reason at all about most of what they do in life, including the stuff that can be very important. Reasoning is generally rather costly in terms of time and energy unless you're used to doing it and that's generally because it's part of your job. And you can only reason about stuff that has already been formalised. Logic itself is a good example of that.
I also agree that there are biases, essentially emotional ones. Once your committed to a particular belief, you will ignore logical arguments to the contrary. However, there's a good reason for that. Logic is garbage in, garbage out. Whatever the validity of the argument, we still don't know whether the conclusion is true simply because we don't know whether the premises are true. So, people are in fact correct to dismiss even valid arguments. And, most people don't know about the formal distinction between valid and sound, they just dismiss the argument wholesale, and again, that's the correct attitude to take. Logic isn't used for discovering the truth. Logic is used to believe the conclusion that follows from a prior belief. If I know your beliefs, I can move you to act logically in accordance with them by using a valid argument. If I know you believe in God and that God asks believers to help their neighbours, I can argue you should help your neighbour. But it won't work if you don't believe in God to begin with. And whether God exists or not is entirely irrelevant. What matters is what you believe is true.
Most people don't use formal logic but all use their inherent logical capacity. Suppose some people are talking about Obama. After ten minutes someone may say, "Well, politicians are just liars". And that's it. Whether you agree with this "rule" and whether you think Obama is himself a liar, indeed irrespective of whether you like or dislike Obama, you will understand what the guy actually didn't even spell out, namely that he meant that Obama is a liar. That's a logical inference and yet, although they will understand what the guy meant, no one present will need to think about it. They will just know what the guy meant without having to think about it. That's entirely intuitive and people don't learn formal logic. They're not even aware they made a logical inference. You yourself don't even understand, given what you say here, that you are making precisely this kind of inference all the time without having to think about it. So, we all have this inherent capacity because without it we could possibly even begin to understand each other.
So, intuition is not to blame. Indeed, we have people trained in formal logic being systematically wrong about whole classes of inference because the formal logic they learn is wrong. As of today, our best logic is our intuitive logic. The brain is a natural. You just need to learn to listen to it and make the distinction between the logical validity of your intuition and the assumptions you make without even realising it. If you're wrong, the likelihood is that some of your assumption are wrong.
EB