Well, first off, if you are upgrading from 5.0 to 5.5, you really need to do this on a test server prior to making the upgrade in a production environment. This will get you comfortable with the steps of upgrading and let you figure out any trouble areas beforehand, which will dramatically reduce your downtime of upgrading.

So to upgrade, I would upgrade from 5.0 to 5.1, then 5.1 to 5.5 as the manual suggests. There will be downtime, but if you do the upgrade steps on a test setup first, you will reduce your downtime dramatically. Make sure you have all the installers downloaded beforehand, don't wait to download them while you're in downtime.

You could do the replication setup as Rolando points out, but please don't do the upgrade on production without testing out the steps first.

MySQL 5.6.10 is quite new to me as well, so bear with me on this answer

I installed MySQL 5.6.10 on a Linux VM

I added default-storage-engine=MyISAM to my.cnf and restarted MySQL

It went from this:

mysql> show engines;
+--------------------+---------+----------------------------------------------------------------+--------------+------+------------+
| Engine             | Support | Comment                                                        | Transactions | XA   | Savepoints |
+--------------------+---------+----------------------------------------------------------------+--------------+------+------------+
| MyISAM             | YES     | MyISAM storage engine                                          | NO           | NO   | NO         |
| CSV                | YES     | CSV storage engine                                             | NO           | NO   | NO         |
| MRG_MYISAM         | YES     | Collection of identical MyISAM tables                          | NO           | NO   | NO         |
| BLACKHOLE          | YES     | /dev/null storage engine (anything you write to it disappears) | NO           | NO   | NO         |
| MEMORY             | YES     | Hash based, stored in memory, useful for temporary tables      | NO           | NO   | NO         |
| PERFORMANCE_SCHEMA | YES     | Performance Schema                                             | NO           | NO   | NO         |
| ARCHIVE            | YES     | Archive storage engine                                         | NO           | NO   | NO         |
| InnoDB             | DEFAULT | Supports transactions, row-level locking, and foreign keys     | YES          | YES  | YES        |
| FEDERATED          | NO      | Federated MySQL storage engine                                 | NULL         | NULL | NULL       |
+--------------------+---------+----------------------------------------------------------------+--------------+------+------------+
9 rows in set (0.00 sec)

to 

mysql> show engines;
+--------------------+---------+----------------------------------------------------------------+--------------+------+------------+
| Engine             | Support | Comment                                                        | Transactions | XA   | Savepoints |
+--------------------+---------+----------------------------------------------------------------+--------------+------+------------+
| MyISAM             | DEFAULT | MyISAM storage engine                                          | NO           | NO   | NO         |
| CSV                | YES     | CSV storage engine                                             | NO           | NO   | NO         |
| MRG_MYISAM         | YES     | Collection of identical MyISAM tables                          | NO           | NO   | NO         |
| BLACKHOLE          | YES     | /dev/null storage engine (anything you write to it disappears) | NO           | NO   | NO         |
| MEMORY             | YES     | Hash based, stored in memory, useful for temporary tables      | NO           | NO   | NO         |
| PERFORMANCE_SCHEMA | YES     | Performance Schema                                             | NO           | NO   | NO         |
| ARCHIVE            | YES     | Archive storage engine                                         | NO           | NO   | NO         |
| InnoDB             | YES     | Supports transactions, row-level locking, and foreign keys     | YES          | YES  | YES        |
| FEDERATED          | NO      | Federated MySQL storage engine                                 | NULL         | NULL | NULL       |
+--------------------+---------+----------------------------------------------------------------+--------------+------+------------+
9 rows in set (0.00 sec)

No problem.

If you placed

default-storage-engine=MyISAM

in my.cnf, restarted MySQL and still the default is InnoDB, then there is only one explanation: You placed default-storage-engine=MyISAM in the wrong part of my.cnf

I once caught a mistake like that in a ServerFault question : Set group_concat_max_len permanently (MySQL config)

Make sure the option is under the [mysqld] section of my.cnf

[mysqld]
default-storage-engine=MyISAM

SUGGESTION

I think MyISAM in MySQL 5.6.10 is run as a plugin. Check your error logs for any plugin errors.

Also, do this:

In one SSH session, tail -f /var/log/mysqld.log

In another SSH session, service mysql restart

Look for any plugin messages associated with MyISAM. For example, note that when I ran a shutdown I saw these messages:

2013-02-26 15:20:13 1725 [Note] InnoDB: Starting shutdown...
2013-02-26 15:20:15 1725 [Note] InnoDB: Shutdown completed; log sequence number 1600309
2013-02-26 15:20:15 1725 [Note] Shutting down plugin 'PERFORMANCE_SCHEMA'
2013-02-26 15:20:15 1725 [Note] Shutting down plugin 'CSV'
2013-02-26 15:20:15 1725 [Note] Shutting down plugin 'MEMORY'
2013-02-26 15:20:15 1725 [Note] Shutting down plugin 'MRG_MYISAM'
2013-02-26 15:20:15 1725 [Note] Shutting down plugin 'MyISAM'
2013-02-26 15:20:15 1725 [Note] Shutting down plugin 'sha256_password'
2013-02-26 15:20:15 1725 [Note] Shutting down plugin 'mysql_old_password'
2013-02-26 15:20:15 1725 [Note] Shutting down plugin 'mysql_native_password'
2013-02-26 15:20:15 1725 [Note] Shutting down plugin 'binlog'
2013-02-26 15:20:15 1725 [Note] /usr/sbin/mysqld: Shutdown complete

130226 15:20:15 mysqld_safe mysqld from pid file /var/lib/mysql/chtn-web2v.pid ended

Note that MyISAM is a plugin. If you do not see anything like

2013-02-26 15:20:15 1725 [Note] Shutting down plugin 'MyISAM'

your MyISAM plugin may have an issue with the Mac OS X version of MySQL.