I'll break this down again further:1) Objectivism ignores the is/ought problem. How so?
In your response from Rand, she states
The fact that a living entity is, determines what it ought to do.
this is utterly ignoring the problem. The problem is that the jump from the way something is to the way something ought to be is not a valid one. Therefore her response to the problem comprises nothing more than "lol wut?" and willful ignorance of what it means for her philosophy. This is a valid concern. 2) Her disdain for altruism runs against studies that show altruistic behavior in primates. No it doesn't. I am sure Ayn Rand would have no problem if someone told her primates showed altruistic tendencies. It wouldn't weaken her philosophy in the slightest.
Frans de Waal and others have pretty conclusively shown that primates act altruistically. They do not need the guarantee or even ability for that altruism to be reciprocated to do good for others. This is a problem for Rand. Assuming her objectivist framework (allowing us to ignore the is/ought problem as well) we can see that humankind's closest relative's state of nature is one of compassion and giving. This means that we do not act solely in self interest. Compare that to John Galt's speech:
This much is true: the most selfish of all things is the independent mind that recognizes no authority higher than its own and no value higher than its judgment of truth. You are asked to sacrifice your intellectual integrity, your logic, your reason, your standard of truth-in favor of becoming a prostitute whose standard is the greatest good for the greatest number
It would seem that altruism and utilitarianism are not acceptable means of living. But, we have seen that this is how we are, and our survival implies (according to Rand) that is how we should be. We should and should not be grounded in altruism. This is a problem.3) She attempts to give a reductive approach to a nuanced problem. (epistemology) And is she wrong? What's the problem of epistemology, and what's the answer?
The problems of epistemology are many. It is a struggle to clearly say what we can and cannot know and how we know it. It is a topic that has been debated for centuries. I don't know the answer but I'd suggest that anyone who ignores the centuries of meaningful debate on the topic is attempting to take a shortcut. We will have more on this. (And yes, this is a problem.)4) Even in an idealized world filled with supermen she seems to forget that some tasks do not require a higher class of individual. I don't see this at all in her fiction or the some non-fiction I have read. She seems perfectly fine with many tasks involving any class of individuals, as long as they do not systematically leech off of others.
My concern is more that if all of the John Galts of the world do make their own society and throw off the 'leechers', they will be forced to do many things that they think are beneath them. They will need to serve. They will need to clean. If capitalism dictates that there are winners and losers, some will be losers. I will readily admit this is less of a concern for Rand than the capitalistic Randroids who want to put her ideals into action without further thought, but for them, this is a problem. 5) Her contemporaries focused on such problems as how language affects our understanding of the world and how the absurd is a necessary condition of the human experience. She instead focused on saying "A is A" through long-winded boring speeches by her characters. But you fail to recognize that she had to harp on this A=A thing because so many otherwise intelligent people seem to ignore it, and it's the basis of her entire philosophy. I cannot recall a single refutation of her beliefs that doesn't either consciously or unintentionally contradict A=A.
This gets me back to #3. What does 'A=A' mean? If that is a meaningful question it means that epistemological concerns are still valid (see 3) and that we need to unpack this statement. If it is a statement of identity, I doubt that anyone wants to 'contradict' it. If it is a statement that things are exactly as they seem, then it seems to utterly ignore problems that have confounded philosophy (and science) for centuries. From the Pre-Socratics to Aristotle to Descartes to Derrida, we have explored the problems of knowing and confronted what we can or cannot know. This is why nobody takes Rand or Randroids seriously.
They also don't taken Randroids seriously because it is easy, very easy
to show the problems with her philosophy and they say things like
I've read her fiction and some non-fiction, and I have met many intelligent people who have a big problem with Ayn Rand and none of them have ever had a valid reason why.
I started this with five quick reasons off the top of my head. I've now defended them from sophomoric shenanigans. These are valid reasons. (Or, prove me wrong)
1. Well, I cannot speak for Rand but I would argue that basically the is/ought problem is precisely what I mean when I say people either consciously or unintentionally undermine A=A. Rand has little patience for rationalizations because they had no meaningful base in reality. The question of what something "ought" to be is irrelevant to what things are and what things do, so of course she didn't address it because she didn't consider it intellectually valid. This is also why she willfully dismisses centuries of philosophers, not because she doesn't understand what they are saying, but more because does understand it and thinks it has no true basis in reality.
I would say this is not a valid reason for dismissing Ayn Rand's philosopy. You may want her to address this issue more, but not doing so does not undermine the validity of her philosophy, it simply makes it incomplete (iyo). How does "ignoring" this problem make a statement or premise of hers conclusively false?
2. As you've already admitted, this is completely tangential and has no bearing on Rand's philosophy. Sooo, we can agree this is not a valid reason then, right?
3. Again, your explanation of this was basically what you accused Rand of earlier, "lol wut?" You're saying that just because she doesn't acknowledge centuries of philosopher we should dismiss her. This, ironically, is a logical fallacy Rand personally exposed and despised when she said something to the extent of: Liberals admire things for the sole reason that they are new, which is preposterous. Worse yet, conservatives admire things just because they are old (I am clearly butchering the quote which is why I didn't put it in quotes, but you get the idea. Just because philosophers have harped on something for centuries says nothing about the validity of that topic).
Again, I conclude this to not be a valid reason to dismiss Rand.
4. This is not at all incompatible with Rand. Clearly in Atlas Shrugged even among the "supermen" there were still levels of superiority. I mean, I'm sorry but is this really an argument? "Lol, if Galt's Gulch existed whose going to mop the floors? luuullzzz." I mean, it's funny to think about, but nothing at all Rand would be concerned about and not in any way contradictory to her philosophy.
Clearly, an invalid reason to dismiss Rand.
5. It is the law of identity. You would be surprised by how many times people contradict it, again without even knowing. This is possible the main reason Rand refused to do debates, because any time her opponent would say something lulzy, she would basically have to school him on the axioms of "A is A" etc. to determine his contradiction in premises that lead to his false belief, etc. This is why she talks about it so often, because so many people claim to accept it yet contradict it.
Anyway, the fact that you do not like that she talks about the Law of Identity again seems completely irrelevant to the actual validity of her philosophy. Therefore, we again have an invalid reason to dismiss her.