<?php
 
$old_arr = array(
    0 => array (
        0 => array(
            'id' => 3,
            'hoge_id' => 15,
        ),
    ),
    1 => array (
        0 => array(
            'id' => 9,
            'hoge_id' => 15,
        ),
    ),
    2 => array (
        0 => array(
            'id' => 13,
            'hoge_id' => 15,
        ),
    ),
    3 => array(
        0 => array(
            'id' => 22,
            'hoge_id' => 15,
        ),
        1 => array(
            'id' => 22,
            'hoge_id' => 15,
        ),
        2 => array(
            'id' => 22,
            'hoge_id' => 15,
        ),
    ),
);
 
$new_arr = array();
$i = 0;
array_walk_recursive($old_arr, function($v, $k) use (&$i, &$new_arr) {
    $new_arr[$k === 'hoge_id' ? $i++ : $i][$k] = $v;
});
 
print_r($new_arr);

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