Appendix. It has been suggested that there is some immunity function from this vestigial colonic appendage. But it often becomes crudely clogged and then infected, necessitating its removal. I propose either redesigning the wee thing so that it doesn't block so easily (perhaps a flush valve?), placing it elsewhere in the body (a more sanitary locale?) or losing the worm shaped poop pouch all together.
Sinuses and eustachian tubes - the openings are too small, the tubes run almost horizontal, fluid can't drain and we are left with a warm, moist cavity = petri dish. Introduce bacteria (tube, meet streptococcus!), and you've got yourself an infection. And then my baby is up all night, screaming and crying. And then my ears hurt. Fix this.
The spine. I'm fond of this structure, it certainly keeps me occupied, but the current design is better suited for walking on all fours than for upright posture. Since the majority of my patients are evolved enough to walk erect, perhaps this is why the majority of my patients also have back pain?
Adult female pelvis. Babies' heads. Might I recommend better size matching?
I could go on. Like how about fixing things like inherently weak arches (70% of us have 'flat feet') and unaccommodating eye lenses so I don't have to accessorize with such sexy accoutrements as orthotics and eyeglasses? Then again, some gentlemen dig nerdy ladies. I don't judge.
I just think that after billions of years, we are due for some updates to the human hardware. Or software... or should that be firmware? Cut me some slack, I'm still using my Commodore 64. Let's get on these Sapien improvements. Isn't there an app for that?