Why does Pac-Man not like to eat eyes?

Solution 1:

The further the eyes are from the ghost pen, the longer it takes for them to reach it and regenerate. This means the time it takes for a ghost to respawn after being eaten is variable.

Because it is variable, the eyes give the player a measurable way to determine when the ghosts are going to respawn (when the eyes reach the ghost pen). If Pac-Man ate the ghosts' eyes, the player would have no visual idea when the ghosts would regenerate, which might be hazardous to Pac-Man's health.

Solution 2:

The eyes are there to give you a respite before the ghost regenerates in the center cage, as others have pointed out. However, it's also important to note that even if you could eat the eyes, you still couldn't! -- because immediately upon eating a ghost, the eyes begin their journey at 2x your speed toward the center cage. Unless there is a bug in the path algorithm, it is impossible for the Pac-Man to ever intersect with the eyes again once they've begun their journey.

Solution 3:

It could be that he wasn't supposed to. I mean, maybe the eyes are there to show that the ghost was eaten, leaving only the eyes behind.

If the eyes were somehow eaten, the how can the ghost spawn back and chase you again? It would be boring if there was only one ghost chasing you right?