This bug (http://bugs.mysql.com/19027) was reported by Peter Zaitsev over two years ago… it may not be critical, but it’s nasty and surely it can be fixed. This is the problem.
If InnoDB incurs a fatal error during initialisation, for instance changing logfile size, or from a typo in another parameter in the config, mysqld still starts but InnoDB will be disabled. According to Heikki, a storage engine cannot make mysqld not start at that stage, so the only option would be to chuck an assertion – frankly, I’d prefer that over the current misbehaviour!
So you can have a running server that kinda looks ok, but not have access to some or all of your tables.
In a word: ridiculous!