Batch File: ( was unexpected at this time

Oh, dear. A few little problems...

As pointed out by others, you need to quote to protect against empty/space-containing entries, and use the !delayed_expansion! facility.

Two other matters of which you should be aware:

First, set/p will assign a user-input value to a variable. That's not news - but the gotcha is that pressing enter in response will leave the variable UNCHANGED - it will not ASSIGN a zero-length string to the variable (hence deleting the variable from the environment.) The safe method is:

 set "var="
 set /p var=

That is, of course, if you don't WANT enter to repeat the existing value.
Another useful form is

 set "var=default"
 set /p var=

or

 set "var=default"
 set /p "var=[%var%]"

(which prompts with the default value; !var! if in a block statement with delayedexpansion)

Second issue is that on some Windows versions (although W7 appears to "fix" this issue) ANY label - including a :: comment (which is a broken-label) will terminate any 'block' - that is, parenthesised compound statement)

You are getting that error because when the param1 if statements are evaluated, param is always null due to being scoped variables without delayed expansion.

When parentheses are used, all the commands and variables within those parentheses are expanded. And at that time, param1 has no value making the if statements invalid. When using delayed expansion, the variables are only expanded when the command is actually called.

Also I recommend using if not defined command to determine if a variable is set.

@echo off
setlocal EnableExtensions EnableDelayedExpansion
cls
title ~USB Wizard~
echo What do you want to do?
echo 1.Enable/Disable USB Storage Devices.
echo 2.Enable/Disable Writing Data onto USB Storage.
echo 3.~Yet to come~.

set "a=%globalparam1%"
goto :aCheck
:aPrompt
set /p "a=Enter Choice: "
:aCheck
if not defined a goto :aPrompt
echo %a%

IF "%a%"=="2" (
    title USB WRITE LOCK
    echo What do you want to do?
    echo 1.Apply USB Write Protection
    echo 2.Remove USB Write Protection

    ::param1
    set "param1=%globalparam2%"
    goto :param1Check
    :param1Prompt
    set /p "param1=Enter Choice: "
    :param1Check
    if not defined param1 goto :param1Prompt
    echo !param1!

    if "!param1!"=="1" (
        REG ADD HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\StorageDevicePolicies\ /v WriteProtect /t REG_DWORD /d 00000001 
        echo USB Write is Locked!
    )
    if "!param1!"=="2" (
        REG ADD HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\StorageDevicePolicies\ /v WriteProtect /t REG_DWORD /d 00000000
        echo USB Write is Unlocked! 
    )
)
pause
endlocal