$kat_ozel = json_decode('[["90"],["88","96"]]');
$kat_ozel_fiyat = json_decode('[["15"],["20"]]');
$new_arr = array();

foreach($kat_ozel as $k => $v){
   foreach($v as $_k => $_v){
      $new_arr[$_v] = $kat_ozel_fiyat[$k][0];
   }
}

print_r($new_arr); // Array ( [90] => 15 [88] => 20 [96] => 20 )