Vague memory from 10+ years ago:
* Getting real deep with detecting OS/instruction set and edge cases
* Constantly validating permissions on every directory and file
* Constantly verifying checksums on everything put in place
* Concurrency controls to make sure the user didn't launch the installer twice, or the system wasn't live running when being reinstalled.
* Dependency verification was it's own rats nest of problems
* Uninstalling
* Logging
* Status tracking (except for really large files things get weird...)
* Aborting/Cancelling install