There may have been several factors that led Crouch Jr. to not simply stun everyone.
Practicality
Remember, the champions are inside the maze while Crouch is outside the maze:
"We are going to be patrolling the outside of the maze," said Professor McGonagall to the champions. "If you get into difficulty, and wish to be rescued, send red sparks into the air, and one of us will come and get you, do you understand?"
Presumably, then, he would only have the opportunity to stun a champion who happened to be near the outer wall where he was patrolling. If a champion was deep in the heart of the maze, Crouch would be unable to stun him/her.
This may in fact be supported by a close reading of Crouch's statement to Harry:
"I was patrolling around it, able to see through the outer hedges, able to curse many obstacles out of your way. I stunned Fleur Delacour as she passed. I put the Imperius Curse on Krum, so that he would finish Diggory and leave your path to the cup clear."
The phrase "able to see through the outer hedges" may indicate that even with the magic eye he could not see very deep into the maze. As such he would not have the opportunity to stun someone deep in the maze. The phrase "as she passed" is perhaps the most telling. Crouch may have only been able to stun Fleur because she passed, i.e. he was able to stun her because she entered into his range. If a champion stayed out of his range, though, he would not have been able to stun him/her.
Perhaps, then, Crouch was unable to stun Cedric because he did not get an opportunity to do so. When he got the opportunity to attack Krum he may have realized that it would be possible for Cedric to entirely avoid him and thus beat Harry to the cup. So Crouch had no choice but to use Krum to chase down Cedric, because he was unable to attack Cedric himself.
Thus, he stunned Fleur when he had the opportunity; he did not stun Cedric because he never got the opportunity; and he did not stun Krum because he needed to use Krum to attack Cedric.
Conspicuity
The stunning spell is generally associated with a strong visual effect. When Dumbledore stunned Crouch:
"Stupefy!" There was a blinding flash of red light, and with a great splintering and crashing, the door of Moody's office was blasted apart —
When the Ministry wizards stunned Winky:
"STUPEFY!" roared twenty voices — there was a blinding series of flashes and Harry felt the hair on his head ripple as though a powerful wind had swept the clearing. Raising his head a fraction of an inch he saw jets of fiery red light flying over them from the wizards' wands, crossing one another, bouncing off tree trunks, rebounding into the darkness —
When the dragon keepers stunned the dragons:
"Stupefy!" they shouted in unison, and the Stunning Spells shot into the darkness like fiery rockets, bursting into showers of stars on the dragons' scaly hides —
This being the case, Crouch may have wanted to avoid stunning Krum and Cedric because the flashes of light would be very conspicuous. The Imperius Curse is never shown to be accompanied by such visual phenomena so it be much less likely that anyone would notice Crouch casting it. (As for why he stunned Fleur instead of using an invisible spell, perhaps he figured that one Stunning Spell would not be so conspicuous, or alternatively, perhaps he only realized how conspicuous it was because he stunned Fleur.)
Suspicious
If all three of the other champions were discovered stunned, it would be pretty obvious that something was going on, and suspicions would be raised. However, making Krum torture Cedric created a believable scenario where the champions fought each other. When the task would end and Cedric would say that Krum tortured him, suspicion would be deflected away from Crouch onto someone else. (Of course, there is the possibility that Krum would insist that he was Imperiused which might raise suspicions again, but perhaps Crouch considered that less likely.)
Unnecessary
As to the point that stunning Cedric would have prevented him from almost touching the cup first, Crouch may not have felt that this was necessary. All Crouch needed was to keep the other champions out of the way for long enough to allow Harry to get to the cup. By the time Cedric was attacked Harry was nearly there. A short altercation would have been enough to ensure Harry's victory. Crouch probably did not count on Harry stopping to help Cedric (despite the fact that Harry stayed behind in the Second Task to save all the hostages).
