COUNT(*) takes ages for InnoDB tables as it actually counts the rows individually when you do it. MyISAM on the other hand keeps an internal counter, which means count(*) is fast, but introduces other problems of its own later on.
When you are volume testing these 2, make sure you try selects/inserts/updates concurrently as MyISAM can (does) have big scaling problems caused by the fact it uses table level locking in some fairly trivial situations, so while individual queries can seem fast in isolation when you introduce other operations you get deadlock hell.
If it helps, as a base rule, you should be using InnoDB unless you know you need MyISAM for some specific reason.