We could simply improve on the current 'design'.
Basic changes would offer a big improvement.
Stuff like, move the brain into the chest cavity. We have this insanely armored bucket at the top end of our bodies that still sucks at protecting the brain.
So, enlarge the chest and stick the brain in there. The head would only still house the sensory organs.
Split the breathing tube from the eating tube ... should be simple enough.
Three spines iso one should solve the verticality problem and hey, why not nerve redundancy? "The fall broke your left ventral spine ... if you break the other two, you'll be paralysed!"
This would also solve loads of problems with the bowels, as you could hang them from a membrane that stretches between the three spines iso basically just dumping them in the abdomen.
Hook ovulation up to the conscious part of the brain ... that ought to put a spanner in the works for patriarchies everywhere.
It would be neat if bodies could be made aware of their own DNA. ie. if the body senses it has XY chromosones, it develops a male body image ... note that this is separate from sexuality. You'd still get people with male bodies who had a sexual preference for other male bodies. But no one would ever feel like they were born in the wrong body. The current system depends on an error prone detecting of certain hormones while in uterus.
Marvel comics stuff like super strenght would be neat, of course, and doable, just look at chimps or orangutans who are, pound for pound much stronger than us. But, would that begin to impair our fine motor skills? I wonder. Also, if you make us able to lift 1000 kilos ... you'll need to reinforce the knees, ankles, pelvis to take the weight.
Speaking of pelvises ... a hinge mechanism like in snake's jaws would solve many of the problems during birth. Though, by moving the brain into the chest, we've already removed the need for a massively huge head, so giving birth will already be less torturous.
How to calculate these things? I have no idea.