I felt the same way for a long time after completing the Water Temple. I was always like, "Did they forget something here?" But perhaps they were thinking more on their feet than we realized. The creature (or Morpha), was said to be the cause. It probably didn't take much time at all to...
This is something that has bothered me as well. However, since Ocarina of Time was really the big selling point for me in the series (the one that really got me hooked, though I started w/ LA), just from a regular player's standpoint at the time, I thought that it meant KP was the reincarnation...