Prophecy, you've asked for scientific rebuttals. I take you seriously--and I take you at your word! None of this is medical advice, mind you, just my view of the relevant literature.
On the question of diet alone, bracketing issues of ethics for the moment, there are well-recognised nutrient deficiencies associated with a purely vegetarian and/or vegan diet. One example from the scientific literature:
https://www.karger.com/Article/Abstract/46689
These can be easily rectified by taking supplements, of course, and I don't think the vit. B problems noted here are in any sense controversial.
I'd suggest that people who are careful about what they eat, vegan, vegetarian, paleo, or otherwise tend to fair better than those who eat as standard American/UK diet (SAUD). That, too, is well established in the literature, and virtually any variation from what we typically consume is an improvement because it reduces sugar, refined carbs, processed foods, trans fats, and probably reduces total calories as well. So if your point is that veganism is healthier than the default diet of most people in the West, I'd say sure.
But if your point is that veganism is nutritionally superior to eating like an omnivore, that's not supported by science. Instead, a careful vegan
can eat better and be more healthy than someone consuming the SAUD. But it is just as possible to be just as healthy on a diet of animal fat and protein, consuming fresh vegetables as a relatively small portion of one's total food intake (and avoiding fruit altogether). And especially if liver and other offal are eaten, this diet doesn't require nutritional supplements, with the caveat that sufficient calcium consumption can be an issue if dairy products are excluded. But that's just as much a problem for vegans as well, with the same solutions.
What I'm getting at here is that it's really hard to say what the optimal diet might be, and it largely depends on exactly what's eaten and exactly what's going on with your body biochemically. Others here have pointed to the startling differences in traditional diets across the globe, and it's not unusual to find some populations eating mostly animal-based food while others thrive on largely plant-based diets.
But the now 'old' bias against red meat as related to health is just that--an old bias that's not standing up that well to rigorous testing. Processed foods--meat or veg--are not ideal. And as far as heart disease, etc., the literature now seems to point to the role of
processed meats, not red meat
per se:
http://circ.ahajournals.org/content/121/21/2271.short
But to be fair, researchers still aren't sure about the cancer risks--especially colorectal cancer risks--of consuming lots of red meat:
https://jamanetwork.com/journals/jama/fullarticle/200150
It's important to control for other variables: smoking, exercise, etc. And as rigorous as these studies can be, that's really hard to do well.
What they seem to support, in general, is that it makes sense to vary protein sources to include lots of fish and poultry, too. But that strikes me, too, as uncontroversial.
My point being that you can certainly defend the ethical superiority of veganism, though there, too, one can summon counter-claims and arguments that run contrary to yours. But in terms of what I took to be your claims about its dietary superiority, I don't think that's an established fact. But I may have misunderstood you in any case, and if I have, offer my apologies if I've mis-stated your view on this.