hmm.. seems like there's so much improvement that could be made - really only limited by one's own imagination/comprehension
Assuming I can target microbiology, I would first modify or replace the krebs cycle so that energy production was self-sustainable for long periods of time, and there were no free radicals generated as end products. This would not only reduce cellular degeneration and curb aging, but it could also reduce/eliminate the need to eat or breathe in oxygen (first step to allowing long-term unassisted space and deep-sea exploration ^^).
In addition, I would modify the cellular reproduction cycle, coding in a more rigorous system for cellular repair that would include the ability for division only as a last-resort. This would preserve bio-material as well as the telomeres of my DNA. I would also add a function for regeneration of telomeres after division, thus extending the lifespan of individual cells perhaps indefinitely.
Since my metabolism and cellular reproduction cycles would be running at a much slower rate, my temperature would also be reduced. This would require the replacement of some organic compounds with elements more resistant to temperature. I would modify my biochemistry so that my skeleton would be formed out of lightweight carbon fiber instead of bone, and my skin/organs would be fortified with graphene. This would give my body the ability to withstand much greater degrees of pressure and temperature variation, as well as provide a framework for increased muscular strength. As for the need for calcium ions in nerve conductivity, calcium could be stored throughout the carbon matrix in specified compartments. I would also modify my circulatory system, replacing my four-chambered heart with a multivalvular syphon. This structure would take less energy to circulate blood through my body.
As for the enhancement of natural abilities.. I would modify my cognitive abilities first, increasing the rate at which electrochemical signals could be transferred in my brain. I would also increase the plasticity of my cerebral cortex and allow for the reproduction of neurons in regions where there were extensive processing or storage needs.
The comment you made about vertebrate eyes makes sense as well. I think that for all the senses I would rewire their connections so that more information could be taken in by the brain and perception would become highly accurate and refined.