$cleanEquation(2+4/3^3) - Output: (2 + (4 / (3 ^ 3)))

Predefined bracket rules are kept, calculated outputs remain intact
$cleanEquation(2+16/4%3+2^4) - Output: ((2 + (16 / (4 % 3))) + (2 ^ 4))
$cleanEquation(2+16/4%(3+2)^4) - Output: (2 + (16 / (4 % ((3 + 2) ^ 4))))

Excessive brackets are cleared. Algebra can be used.
$cleanEquation((n+(((2-y)))^2+3)) - Output: ((n + ((2 - y) ^ 2)) + 3)

Supports negative values, simplifies clusters
$cleanequation(4+--16/4-+--+++-++-3) - Output: ((4 - (-16 / 4)) - -3)

Update June 2017: Fixed some ordering to match mIRCs presedence

alias cleanEquation {
  var %f = $1-
  if ($count(%f,$chr(40)) != $count(%f,$chr(41))) %f = $iif($v1 > $v2,%f) $str($iif($v1 < $v2,$chr(40),$chr(41)) $+ $chr(32),$abs($calc($v2 - $v1))) $iif($v1 < $v2,%f)
  var %e = $chr(40) $cleanseEquation(%f) $chr(41), %x = 1, %p, %count = 0, %abc = 161, %signs = $+(^,*/,$chr(37),+-), %q, %abcd, %y, %m, %t
  while ($numtok(%e,32) > 1) {
    %p = $gettok(%e,%x,32)
    if (%p == $chr(40)) {
      inc %count
      var %count [ $+ [ $+(_,%count) ] ] %x
    }
    elseif (%p == $chr(41)) {
      var %abc [ $+ [ $+(_,%abc) ] ] $gettok(%e,$+($($+($chr(37),count,_,%count),2),-,%x),32)
      %e = $iif($+($($+($chr(37),count,_,%count),2)) > 1, $gettok(%e,$+(1,-,$calc($($+($chr(37),count,_,%count),2) - 1)),32),$null) $chr(%abc) $gettok(%e,$+($calc(%x + 1),-),32)
      %m = $remove(%e,$chr(32))
      if ($calc($count(%m,$chr(40))) > 1) && ($calc(($len(%m) - $count(%m,$chr(40))) * 2) <= 1) {
        %t = $calc($pos(%e,$chr(40),$pos(%e,$chr(40),0)) + 1)
        %e = $chr(40) $mid(%e,%t,$calc(($pos(%e,$chr(41),1) - 1) - %t)) $chr(41)
      }
      inc %abc
      %x = 0
      %count = 0
    }
    inc %x
  }
  while (%abc > 161) {
    dec %abc
    %p = $replace($($+($chr(37),abc,_,%abc),2),$str($chr(40),2),$chr(40),$str($chr(41),2),$chr(41))
    if ($numtok(%p,32) == 3) && ($gettok(%p,2,32) !isnum) %p = $gettok(%p,2,32)
    %abcd = 261
    if ($numtok(%p,32) > 5) {
      %y = 1
      while (%y <= 5) {
        %x = 1
        while (%x <= $numtok(%p,32)) {
          %q = $gettok(%p,%x,32)
          if (%q isin $mid(%signs,%y,$iif(%y == 1,1,$iif(%y == 2,3,2)))) {
            var %abcd [ $+ [ $+(_,%abcd) ] ] $+($chr(40),$chr(32),$gettok(%p,$+($calc(%x - 1),-,$calc(%x + 1)),32),$chr(32),$chr(41))
            %p = $gettok(%p,$+(1,-,$calc(%x - 2)),32) $chr(%abcd) $gettok(%p,$+($calc(%x + 2),-),32)
            inc %abcd
          }
          else inc %x
        }
        inc %y $iif(%y == 1,1,3)
      }
      while (%abcd > 261) {
        dec %abcd
        if ($numtok(%p,32) == 3) && ($gettok(%p,2,32) !isnum) %p = $($+($chr(37),abcd,_,%abcd),2)
        else %p = $replacecs(%p,$chr(%abcd),$($+($chr(37),abcd,_,%abcd),2))
      }
    }
    %e = $replacecs(%e,$chr(%abc),%p)
  }
  %e = $iif($regsubex(regextest,%e,\(([^()]|(?R))*\),$null),$+($chr(40),%e,$chr(41)),%e)
  return $replace(%e,$+($chr(40),$chr(32)),$chr(40),$+($chr(32),$chr(41)),$chr(41))
}
alias cleanseEquation {
  var %t, %s = $replace($remove($chr(40) $1- $chr(41),$chr(32)),$chr(41),$scc($chr(41)),$chr(40),$scc($chr(40)))
  while (%s != $replace(%s,**,*,^^,^,$str($chr(37),2),$chr(37),//,/,++++,++,----,--,-+-+,-+,+-+-,+-,++-+,-+,--+-,+-,-++-,+-,+--+,-+,+---,+-,-+++,-+,++--,--,--++,++,+++-,+-,---+,-+)) %s = $v2
  %s = $replace(%s,+-+,+,+--,+-,+++,+,++-,+-,-++,+,-+-,+-,--+,+,---,+-,-+,-,^--,^,*--,*,$+($chr(37),--),$chr(37),/--,/,^+-,^-,*+-,*-,$+($chr(37),+-),$+($chr(37),-),/+-,/-)
  %s = $replace(%s,$scb(--),$scb($null),$scb(+-),$scb(-),$scb(++),$scb($null),$scb(-+),$scb(-),++,+,-+,-,*-,* $chr(512),+-,+ $chr(512),--,- $chr(512),/-,/ $chr(512),^-,^ $chr(512),$+($chr(37),-),$chr(37) $chr(512),$+($chr(40),$chr(160),-),$chr(512),$+($chr(40),$chr(160),+),$null,-,$scc(-),*+,*,^+,^,$+($chr(37),+),$chr(37),/+,/)
  return $replace(%s,+,$scc(+),^,$scc(^),%,$scc(%),*,$scc(*),/,$scc(/),$chr(512),-,$chr(513),+,$chr(160),$chr(32))
}
alias -l scc return $+($chr(160),$1,$chr(160))
alias -l scb return $+($chr(40),$chr(160),$1)