It could be that too many things in the registry are still there that are not installed and therefor slows down the PC on boot since it tries to start them when they are not present anymore. But most of the time a PC will get slowed down due to many factors.
Spyware, malware, virus, too many things running, a application taking up to many resources.
Easiest way to clean up the registry is with either CCleaner
or Glarysoft Registry Repair