The low-hanging Cro-Magnon fruit
The easiest way to “optimize” the human body would be to turn off the genes we inherited from self-domestication and physically return to the types of bodies seen in Cro-Magnons and Neanderthals. Cro-Magnons and Neanderthals could withstand much more punishment than modern humans, with many individuals surviving injuries that would cripple modern humans. Humans are incredibly fragile compared to our ancient relatives, our bones are a lot thinner and we’re overall physically weaker. This is likely related to the suite of domestication genes that occur in humans and produce the symptoms of “domestication syndrome” that we see in dogs versus wolves, cattle versus aurochsen, sheep versus wild sheep, etc.
It would also result in an increase in brain size: species without domestication genes across the board exhibit larger brains and better problem-solving abilities, but at the cost of the parts of the brain that regulate social cognizance and ability to socially communicate are proportionally less developed. Island-dwelling species often exhibit domestication syndrome because in large social groups where individuals have little ability to escape maintaining social cohesion and amiability is key to stop everyone from killing each other. To paraphrase Wrangham "if you put a bunch of stranger humans or bonobos [species with domestication syndrome] they get along, if you put a bunch of chimps or gorillas in a room they kill each other".
Warning: Side effects of turning these genes off will likely result in an increase in aggressiveness and antisociability and a decrease in “agreeableness” and dislike of large crowds or social situations. Such a human would likely act like an individual on the autism spectrum at best. If you do this enjoy your resulting autistic supermen.
Strengthening muscles
Another low-hanging fruit would be strengthening muscles. Chimpanzees are a lot stronger than humans, largely due to greater amounts of fast-twich fibers in their muscles. However, the trade off is that chimpanzees tire out more quickly than humans, who can famously work and walk for hours without getting tired.
Another reason why chimpanzees are so strong is that they have smaller brains. Our brain takes up about 20% of our total metabolic budget, and we actually have special glucose channels in our cells to ensure that our muscles don't hog so much energy we can't support our energy-hungry brain and die. The trade off is that our muscles are incredibly weak compared to other animals of similar size. It's not that chimpanzees are strong, it's that compared to every other species humans are weak and may as well be made of plasticine. However, adjusting this problem would result in humans without human-level intelligence.
Similarly, be careful with how much you thicken bones. Humans have notoriously thin bones compared to other large animals, with thin walls and extensive trabeculae that in cross-section make them resemble styrofoam. But this may be an adaptation to make our bodies more flexible when walking bipedally, bipedalism involves a left-right "sway" to the spine, torso, hips, and shoulders that isn't present in quadrupeds. If the bones can't "bend" slightly, they start grinding against each other and increase the risk of rupturing cartilage and causing arthritis.
Give us back our fangs, please
All catarrhine primates are characterized by a C-p3 honing complex, where the upper and lower canines form sharpened blades by grinding against either the lower third premolar or the upper canine, respectively. All catarrhines, that is, except humans. We lost ours early in human evolution, with a vestigial honing complex being present in Ardipithecus kadabba before being outright gone by the time of Ardipithecus ramidus. This basically means humans threw out our one natural weapon, but the genes should still be there and easy to recapitulate.
Give us back our regeneration, as well
All osteichthyes (bony fishes) are characterized by the ability to regenerate. This includes most fishes and amphibians. Amniote tetrapods notably originally had the ability to regrow limbs, but lost it in favor of an inflammatory response and just duct-taping the injured region with scar tissue. However, the genes for regeneration are still present in all amniotes (including humans), they just have to be turned on and possibly repaired to fix fragments that have degraded into pseudogenes. This is a hot topic in genetic and developmental biology right now.
Warning: Regeneration can come with drawbacks. If the cells around the regenerating tissue are damaged and cannot coordinate with one another, it results in things like this (in this case, a parasite disrupted the developing legs of the frog as a tadpole). One reason why amniotes lost regeneration is that if your limbs only develop once it reduces the chances to screw up.
Restore polyphyodont dentition
Polyphyodonty, otherwise known as the presence of multiple replacement teeth per tooth locus, characterizes most animals like sharks and reptiles. Except mammals. Mammals are diphyodont, which means they have a set of baby teeth (sometimes) and adult teeth and that's it. This causes huge problems because larger mammals can easily wear out their only set of teeth and starve to death. Tweaking human genes to give us one or more pairs of replacement teeth would be a big help.
Childbirth
Childbirth is an absolute circus in humans. The problems with the human method of childbirth are legion, and there are probably umpteen-billion different solutions to fix it. Notably, human gestation doesn't appear to be constrained solely by the head size of the infant, but the infant's metabolic cost on the mother.
Adaptations already in humans
There are already beneficial adaptations in humans that haven't spread throughout the entire population. For example lactase persistence in Indian, African, and European populations, adaptations to increased breathing efficiency in Tibetans, Ethiopians, and Andean highlanders, adaptations to fasting in Polynesians and African-Americans (but notably not the African populations which they came from), and so on and so forth.
The problem with this is it would cause a colossal ethical uproar, much moreso than engineering humans to regrow limbs, have fangs, and multiple sets of teeth. Imagine how easily it could be spun as imperialistic eugenics. "Giving Native Americans, African-Americans, and east Asian populations the ability to enjoy ice cream by genetically editing them to have genes from white people" sounds absolutely horrifying (even if the allele actually came from one of the African populations like in Kenya or Tanzania). Alternatively, "genetic imperialism" by the wealthy countries that have access to gene-editing technology editing themselves to have genes primarily found in groups living in poorer countries (e.g., the oxygen efficiency genes are all found in developing nations and Tibet).
Tradeoffs
Another thing to consider is that there are no "optimal" traits in evolution. "Survival of the fittest" doesn't mean "survival of the best adaptations", it means survival of whatever adaptations happen to work the best within the context of the present environment. Humans are the perfect example of this. We are a species that has a hugely costly brain, a warped spine, poorly built jaws, ridiculous reproductive habits, and are some of the slowest and physically weakest members of the animal kingdom, yet it is Homo sapiens that is currently the dominant megafaunal organism on the planet.
A good example of how this applies to genetically engineered humans more generally is in the novel Cretaceous Sea. One of the protagonists of the novel is genetically engineered to have a super-high metabolism and never get fat. Under plentiful conditions this gene is advantageous because it prevents obesity, but when the characters get stranded in the post-KT late Cretaceous she becomes a huge liability because she has to eat twice as much to survive in an environment where there is little food.
No adaptation works optimally in every environment, and many adaptations are mutually exclusive in usefulness. For example long limbs are optimal in open environments because they allow for faster movement, but they come with the trade-off that proportionally longer limbs are physically weaker due to decreasing the in-lever/out-lever ratio that the muscles that attach to the legs use. Erect limbs are useful in flat-land locomotion but sprawling, lizard-like limbs are more optimal for locomoting over uneven territory.
Balancing the Energy Budget
The biggest thing that you seem to be missing in your question is that there is an additional factor in optimization that is the reason why humans don't already exist in an "optimal" form. Nothing in life is free. In economics that cost comes in the form of time and money, in biology that cost comes in the form of calories and metabolic energy (and to a lesser degree gestation and maturation time). Those calories either have to come from the mother or be provisioned somehow. Want to give your humanoids a super-stomach that can digest any food? Costs calories. A super-kidney that reclaims almost all water? Costs calories. As mentioned before our brain, which is probably the best example of a "super organ" in humans, eats up 20% of our total metabolic budget. You have to balance your energy budget, in order to "optimize" an organ you either have to cut funding to some other part of the body or increase caloric intake.
This is why real animals don't go around "optimized" all the time. You can add all the bells and whistles you want to make a species the best at everything, but you'd basically have to eat super-calorie-dense foods or guzzle rocket fuel to get the energy to support it. After a point you would need so many calories you'd either have to be eating 24/7 or you couldn't survive without highly nutrient-dense artificial foodstuffs. No species has an unlimited energy budget to get things done, so evolution has to pick and choose (in a metaphorical sense, not an intelligent design one) which adaptations they favor.
