Respiratory: Uni-direction, air-sac lungs (all that is needed is two airsacs) and separate throat and larynx so that breathing is possible while swallowing (chockings become impossible). Air-sac lungs are estimated to be 3 times as efficient as our pitiful mammalian lungs be mass of tissue, it is why dinosaurs probably took over during the hypoxic (half the oxygen partial pressure of today) Triassic and why birds can fly over mount everest while people die just climbing it.
Circulatory: why not many small hearts across the body, I could envision 2-chambered hearts for each appendage and for each lung (6 total, 7 for if we include one for the head, maybe and 8th for the lower organs) if a heart fails blood should flow straight through it by pressure from the other hearts.
Reproductive: internal testicles with core body temp spermatogenesis (also like birds). Internal re-absorption of menses in women (no menstruation), heck no ovulation unless mentally commanded, integrate ovarian tissue into uterus lining thus eliminate openings into the abdominal cavity via fallopian tubes. Could even create a 4th hole a "C-section hole" that by-passes the vagina (which frankly is meant to hold a penis not for pushing out babies) and the hips, make it only form at late stage of pregnancy. While we are at it why not a system for simultaneous orgasms? Add some receptor in the vagina for detecting ejaculated semen that cause orgasm. Get ride of the clitoris put those nerves in the vagina. The problem is male and female reproductive tracks share most of the same tissue types and thus have common base parts. If genes for male reproductive organs and female reproductive organs were on the sex chromosomes and not autosomes we could remove common tissue types between gender, no clitoris on women, no foreskin for men (or why not a full foreskin or even a retractable penis that does not hang out and get caught on things?) no nipples on men. Or we could just make everyone hermaphodites with both sets of genitalia, "dick girls", twice the fun, twice the datable population, no gender social oppression, no homophobia.
Immune system: absolute nightmare of over complexity, we could make a passive immune system be re-engineering basic biomolecular systems like ribosomes and then producing a molecule that jams all natural ribosomes. passive immune systems would consume much less energy and not be able to cause autoimmune disorders.
Metabolism: make humans able to produce cellulase enzyme natively and maybe a second stomach and we could get plant matter. Engineer in nitrogen fixation and ability to produce all vitamins and we could live on a diet of nothing but paper if need be.
