Problems upgrading from MySQL 5.1 to MariaDB

Website doesn't state anywhere that MariaDB should be running when executing upgrade_mysql; this is a problem because upgrade_mysql doesn't give any useful diagnostic either.
Getting MariaDB running after upgrade is another problem. The original my.cnf with any possible customizations is wiped out, with no .rpmnew or .rpmsave, so any critical settings need to be restored from backups.
There is one setting where restoration of old values doesn't help:
131109 14:51:16 [ERROR] InnoDB: auto-extending data file ./ibdata1 is of a different size 640 pages (rounded down to MB) than specified in the .cnf file: initial 768 pages, max 0 (relevant if non-zero) pages!
131109 14:51:16 [ERROR] InnoDB: Could not open or create the system tablespace. If you tried to add new data files to the system tablespace, and it failed here, you should now edit innodb_data_file_path in my.cnf back to what it was, and remove the new ibdata files InnoDB created in this failed attempt. InnoDB only wrote those files full of zeros, but did not yet use them in any way. But be careful: do not remove old data files which contain your precious data!
Only after adding the "default" setting of "innodb_data_file_path=ibdata1:10M:autoextend" MariaDB would start, allowing running upgrade_mysql. However, after running upgrade_mysql and restarting MariaDB, connections fail with:
ERROR 1524 (HY000): Plugin 'N' is not loaded
According to http://bugs.mysql.com/bug.php?id=60432 plugin-column used to be fixed in MySQL, and if columns are re-arranged wrong column is read. Logins started working after executing:
ALTER TABLE user CHANGE `is_role` `is_role` enum('N','Y') CHARACTER SET utf8 NOT NULL DEFAULT 'N' AFTER `password_expired`;

Reporting this as one since the issues are quite related, and upgrade path from RHEL6 is likely to be very important. If the recommended upgrade path is MySQL 5.1 -> MariaDB 5.5 -> MariaDB 10.0, I couldn't find any mention of this in documentation. From memory I experienced the configuration overwrite and InnoDB tablespace issues when upgrading from MySQL 5.1 to MariaDB 5.5, only the grant table column issue seems new for 10.0.