Trends in Storage Engine Usage
In the first years of MySQL growth, early web-based applications didn't push the limits of concurrency and availability. In 2010, hard drive and memory capacity and the performance/price ratio have all gone through the roof. Users pushing the performance boundaries of MySQL care a lot about reliability and crash recovery. MySQL databases are big, busy, robust, distributed, and important.
InnoDB hits the sweet spot of these top user priorities. The trend of storage engine usage has shifted in favor of the more efficient InnoDB. With MySQL 5.5, the time is right to make InnoDB the default storage engine.
Consequences of InnoDB as Default MySQL Storage Engine
Starting from MySQL 5.5.5, the default storage engine for new tables is InnoDB. This change applies to newly created tables that don't specify a storage engine with a clause such as ENGINE=MyISAM. (Given this change of default behavior, MySQL 5.5 might be a logical point to evaluate whether your tables that do use MyISAM could benefit from switching to InnoDB.)