The landscape is already a bit weird in terms of "out of the box" features for MySQL because there are at least a few major distributions between Oracle MySQL, Percona XtraDB, MariaDB, etc. They're generally all compatible. They have some different defaults, and very rarely different features. But particularly for XtraDB you tend to get access to better diagnostic info and some better defaults for InnoDB (or at least you used to, my info may be a year or two out of date at this point).
While it is true that MySQL support for online DDLs has gotten much better over the years, I think the tools like pt-online-schema-change are still extremely valuable - there are still certain kinds of changes that you can't make with an online DDL in MySQL, or sometimes you specifically don't want to take that approach. But I'd think of the Percona Toolkit stuff as more a nice set of tools to have in your DBA toolkit, rather than an essential part of your DBMS for anyone running it in production. Its not like the pgbouncer situation. Everybody wants to avoid process-per-connection, but plenty of people can get by without complex online schema migrations.
While it is true that MySQL support for online DDLs has gotten much better over the years, I think the tools like pt-online-schema-change are still extremely valuable - there are still certain kinds of changes that you can't make with an online DDL in MySQL, or sometimes you specifically don't want to take that approach. But I'd think of the Percona Toolkit stuff as more a nice set of tools to have in your DBA toolkit, rather than an essential part of your DBMS for anyone running it in production. Its not like the pgbouncer situation. Everybody wants to avoid process-per-connection, but plenty of people can get by without complex online schema migrations.