I've never been strongly moved by Plantinga's EAAN's general sceptical conclusions allegedly following from naturalism and evolution. It has seemed to me that on the best causal (sketches of) accounts of intentionality, it's pretty much guaranteed that a significant portion of our empirical beliefs are true. I have serious problems with these causal accounts, but given the accounts, EAAN does not appear that persuasive to me.
However, I think one can use EAAN-type arguments for a more limited conclusion, namely that if naturalism and evolution are true, then certain important kinds of knowledge are seriously threatened, specifically moral (and maybe more generally normative) knowledge (I think certain kinds of modal and metaphysical knowledge are also threatened, and it may be that metaphysical naturalism falls within the class of threatened knowledge).
The standard naturalistic evolutionary story about how we get moral beliefs is something like this. Certain kinds of beliefs about what one ought to do promote the fitness of communities and individuals. Consequently, as a result of certain mimetic and/or genetic evolutionary processes, we have roughly the moral beliefs we do. There might be causal intermediaries like propensities for making certain kinds of moral inference.
But notice a crucial difference between this explanation and evolutionary explanations of our ordinary empirical beliefs. In the ordinary empirical case, Plantinga's critics can say we are selected for propensities to have tiger-presence beliefs in the presence of tigers, because there is an obvious fitness benefit from having such beliefs when the beliefs are true. One might worry about details here, but the story has an initial plausibility. However, in the case of moral beliefs, the benefit of having the beliefs does not come from the beliefs' being true.
In the moral case, assuming naturalism and evolution, at best we have a Gettier case instead of knowledge. If we are lucky, there is a large overlap between those moral beliefs that promote fitness and those moral beliefs that are true. Our moral beliefs, based as they are on natural propensities to believe, may be justified. But they are not knowledge, because the connection is too coincidental on this story.
To see that the connection is coincidental, consider this story that is meant to be parallel to the story about moral beliefs. Outside of our community, there is a dark forest. People who go deep into the forest never come back. Eventually, we evolve (mimetically and/or genetically) a propensity to believe that the depths of the forest are full of tigers, and this propensity keeps us out of the forest. In fact, there are tigers deep in the forest, but they are nice tigers and never eat people. The reason people who went deep into the forest never come back is not because the tigers ate them, but because boa constrictors killed them. Maybe we have a justified and true belief that there are tigers in the forest, but it is at best a Gettier case.