One possibility would be to modify the urinary system to output its waste into the GIT, but caution has to be taken to limit the risk of infection. Since we are bipedal, our circulatory system has to work much harder to pump blood vertically. Unlinking the fibrinogenic system from adrenaline control would definitely lower the incidence of cardiovascular disease. Breathing The human breathing system has some drawbacks, primarily the risk of choking on food. A uniflow system would be much smaller, but would loose heat and water faster than our current countercurrent system.
Aquatic breathing is a classic idea.
One possibility would be reserve air storage, for example by improved red blood cells and myoglobin. But the main problem is getting rid of carbon dioxide. It is surprisingly flexible, but might still be improved judging from the number of cesarian sections and deaths at birth in general. A radical solution would be to use a pouch instead, like kangaroos. Some people might like genital taste buds and other improvements in innervation.