Well this is the first thing that comes in my mind so you could try this:

Code (Text):

1.  

Code (Text):

1.  
2. on join:
3.     set {Cooldown::%player%} to false
4. #Fireball Shooter
5. on rightclick holding a blaze rod:
6.     if {Cooldown::%player%} is false:
7.         play sound "entity.blaze.shoot" with volume 1 to the player
8.         make the player shoot a fireball at speed 4
9.         set {Cooldown::%player%} to true
10. every 3 seconds:
11.     loop all players:
12.         if {Cooldown::%loop-player%} is true:
13.             set {Cooldown::%loop-player%} to false
14. on rightclick holding a blaze rod:
15.     if {Cooldown::%player%} is true:
16.         cancel event
17.         send "&cYou are on cooldown!"
18.  

Haven't tested it but it should work.

 

Please, don't use true/false, use true/not set instead. Means that if it's not true, you clear the variable. It's good for your server's performance.

 

Code (Text):

1. variables:
2.     {Cooldown.%player%} = 0
3.  
4. on rightclick holding a blaze rod:
5.     if {Cooldown.%player%} = 0:
6.         set {Cooldown.%player%} to 1
7.         play sound "entity.blaze.shoot" with volume 1 to the player
8.         make the player shoot a fireball at speed 4
9.         wait 3 seconds
10.         set {Cooldown.%player%} to 0
11.     elseif {Cooldown.%player%} = 1:
12.         message "&cYou have to wait 3 seconds to shoot a fireball!" to player
13.        
14.  

this should work (not tested)