The script you've created is around 1600 lines. This would be fine if it wasn't for the fact that there is a massive (and I mean MASSIVE) amount of useless command duplication. For example, you created a command called /vanish and then created a separate command called /v with exactly the same function. Use aliases, not an extra 20 lines per each command.

Code (Skript):

1.  
2. command /vanish [<player>]:
3.    aliases: /v
4.    trigger:
5.       #do stuff
6.  

Not very hard to do ^

As well as this, you've taken up more space on recreating mechanics that are already done for you in Skript.

e.g:

You created a freeze command:

Code (Skript):

1. command /freeze [<player>]:
2.     aliases: /ss
3.     permission: essentialsa.freeze
4.     permission message: {@error-prefix} {@no-perms-message}
5.     trigger:
6.         if arg-1 is not set:
7.             message "{@error-prefix}&7 /freeze <player>"
8.             stop
9.         if arg-1 is set:
10.             if arg-1 is command sender:
11.                 message "{@error-prefix} &7You cannot freeze yourself!"
12.                 stop
13.             if {freeze.%arg-1%} is not set:
14.                 message "{@freeze-prefix} &7You have froze &3%arg-1%&7!"
15.                 message "{@freeze-prefix} &7You have been frozen!" to arg-1
16.                 message "{@freeze-prefix} &7Please join TeamSpeak! IP: &3{@Teamspeak}" to arg-1
17.                 set {freeze.%arg-1%} to location of arg-1
18.                 stop
19.             else:
20.                 message "{@freeze-prefix} &7You have unfroze &3%arg-1%&7!"
21.                 message "{@freeze-prefix} &7You have been unfrozen!" to arg-1
22.                 clear {freeze.%arg-1%}
23.                 stop
24.  
25. on any movement:
26.     if {freeze.%player%} is set:
27.         teleport player to {freeze.%player%}
28.         stop

However, you could've saved more than 10 lines by just using the effect:

Code (Skript):

1. set freeze state of player to true

Finally, you could've used just one variable for this entire script. By using loads of little and randomly named variables (e.g "{freeze.%arg-1%}"), it makes it almost impossible to clean up the script / remove all variables.

You could've done every single variable in one list variable:

Code (Skript):

1. {EssentialsA::freeze::%arg-1%}
2. {EssentialsA::warps::%arg-1%}

That way, if I wanted to clean / clear up the script, all I need to do is:

Code (Skript):

1. delete {EssentialsA::*}

All in all, I think you should try doing much smaller projects. It is clear that you do not have a lot of experience in Skript (Not an insult, everyone was there once.). Trying big projects like this often lead to inefficient or broken scripts. I see that you've put a lot of effort into this and I respect that but you should start small and slowly expand upon your Skript knowledge.

 

It's good but aliases won't work essentials will override it.

 

What's the point in downloading an Essentials script and having the Essentials plugin...? Isn't this supposed to replace it?

 

Not replacing it, I would put it as an addon. Sorry for any confusion.

 

But every single command it has is in Essentials, making it a replacer...?