decreased performance of stored procedure when migrated from mysql server 5.0 to 5.5
If all your data is InnoDB, I have a surprise for you.

It is a little-know fact, but there are some occasions when an older version of MySQL/InnoDB can outrun/outgun a newer of MySQL/InnoDB. How can that be possible?

I wrote about this in DBA StackExchange before


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You will have to perform some due diligence in configuring MySQL to harness more threading and more CPUs.