Does it really matter if the default storage engine is InnoDB? My default storage engine is MyISAM
Yes, there are many differences. The biggest for me is that InnoDB supports foreign keys MyISAM does not.
Some will argue that MyIsam is faster for reads, but if you want to take advantage of compression for example you need Innodb.
My default position is to start with InnoDB whenever possible, then if you cannot use this for example when using spatial features then use MyISAM.
The most concise post on this can be found over at Percona.
Hope this is of use