MySQL Upgrade on Windows
Actually, this plan is kind of dangerous for the mysql schema. Why ?

You are upgrading two versions up. mysql_upgrade will not respond well to this. I have a post where someone upgraded without addressing mysql.user : Any known issues upgrading from MySQL 5.1.73 to 5.6.21?

I have old posts on how to upgrade two versions in one shot


Apr 11, 2013 : MySQL upgrade 5.0.88 to latest (Best Reference)
Feb 08, 2012 : will replication from 5.5.20 to 5.0.XX server work?
Jul 26, 2011 : Restoring an old backup to latest MySQL release


Here is an additional post on how to move the grants with pure SQL : Upgrading mysql myisam 5.1 to mysql 5.6: force innodb on restore?. That post is based on Linux.

To do it in Windows, here are the steps

STEP 01 : Run This

set MYSQL_USER=root
set MYSQL_PASS=rootpassword
set MYSQL_CONN=-u%MYSQL% -p%MYSQL_PASS%
set SQLSTMT="SELECT CONCAT('SHOW GRANTS FOR ',QUOTE(user),'@',QUOTE(host),';')
set SQLSTMT=%SQLSTMT% FROM mysql.user WHERE user&lt;&gt;''"
mysql %MYSQL_CONN% -ANe%SQLSTMT% &gt; GetGrants.sql
echo "SET sql_log_bin = 0;" &gt; MySQLUserGrants.sql
mysql %MYSQL_CONN% -AN &lt; GetGrants.sql &gt;&gt; MySQLUserGrants.sql


STEP 02 : Append a semicolon to every line in MySQLUserGrants.sql

STEP 03 : Load MySQLUserGrants.sql into MySQL 5.6 setup