I may not actually be much of a Sektor-player, but I can appreciate his classic no-nonsense throw-animation. 
Just grab and throw. 

Most other characters have some really long-winded animations that seem... I donno... un-realistic?! 
That's probably not really the word I'm looking for because it is Mortal Kombat after all... 
I guess it's all in making throws that fit the different character's powers, but most of them seem like something the one who's being thrown could easily break out off with the time it takes to pull off. 

...And I guess I could see how characters like Sub-Zero and Cyrax could abuse a faster throw-animations - but still... 
 
*minor rant over*

I never liked Scorpion's throw, probably the goofiest one I can think of off the top of my head. It looks kind of awkward.

Sonya's is also pretty long.

I agree that throw's shouldn't be longer than a second in any game, but in this one the X-Rays also take a while to animate as well.

Stryker's was always the one that struck me as overlong (likewise his X-ray). Everyone else's is fine. A bit theatrical, maybe, but it adds to the flavor of the character to have more than just a simple grab/toss.

I hate anything in the game that just makes me want to put my controller down, cross my arms, or tap my feet. That long Sonya throw with the accompanying "Yes!" just pisses me off. 
 
Ermac comes to mind too.