Well, there is a plausible case to be made that Feser tends to overstate Thomism's priority in scholasticism. See the Scotist critiques of Scholastic Metaphysics at The Smithy. The basic complaint, apart from disputing of substantive philosophical theses, is that Feser titled the book Scholastic Metaphysics, when it really defends neo-Thomist metaphysics, with a few jabs toward Scotus and Ockham. They point out that it is somewhat a matter of historical accident that Aquinas has the prominence he has (and which he didn't quite have in the medieval period after his death), although they concede that Aquinas is a good spot to start studying medieval philosophy because he is easy to read and widely translated, unlike others. Feser more or less conceded these points in his response but claimed it was still appropriate to call the book "scholastic".

There is always going to be latitude in how one reads the history:

The high medieval critics of Thomism, from both the more theologically conservative Augustinian side and the more progressively secular side often grouped under the rubric of Latin Averroism, had important objections that brought up what seem plausibly to be significant problems in Thomas' philosophy. And the successive generations of philosophers looking for a more sustainable solution to the intellectual problems of the time--from the Scotists and nominalists to the humanists and new Platonists, to the rationalists and the empiricists--defended powerful, systematic accounts of philosophy plausible on their own grounds, which merit being taken seriously.

Were the objections decisive and accurate? Well, maybe, maybe not. You could read the history of the response to Scotism, humanism, nominalism, rationalism, and empiricism in this way too. They faced some tensions, lots of people responded with "powerful, systematic accounts of philosophy plausible on their own grounds." If you describe the critiques as "successful" (like Kant's critique of the cosmological argument, apparently), then well, you don't have to look at the arguments.

I do think the responses and alternatives to Thomism "merit being taken seriously." I don't think some sort of historical error theory (Aquinas was right, people misunderstood Aquinas, believe him now) is sufficient to defend him. But I don't think any of his defenders think that either.

Was Thomism misrepresented? Sometimes. Largely modern philosophers did not respond to it, since they were receiving some sort of watered down scholasticism. Is this because Thomism had already revealed itself to be a failure? Maybe, maybe not. The history of philosophical progress is not generally linear. The root of Cartesianism and Humeanism finds less sympathy today after Wittgenstein's critiques, which have some affinity with Aquinas. People are much more inclined to do systematic metaphysics and on independent grounds have moved in the directions of powers, essences, etc. Aquinas has provided the backbone of some contemporary action theory and virtue ethics.

I do someone sympathize with your interlocutor on a final point. Elizabeth Anscombe is reported to have, on separate occasions, told her daughter and David Braine to use Aquinas's ideas without naming him, because both those sympathetic and those not "turn off" when they hear that he defended some point in question. I think that is right, and I think there are risks to leaning too much on someone's name, as seems to me to happen in some Catholic circles. People (excepting new atheists) also tend to "go easier" on older philosophers in the sense of finding charitable ways to read them and not flatly rejecting theses they find very implausible. I think there are advantages to be had by trying to defend Aquinas without naming him, not the least of which is that you don't have to get mired in these debates over whether he was defeated or misrepresented or ignored or what.