One of the things I try to make everyone aware of when upgrading from 5.0 -> 5.1+ is the change in some of the charset/collations that happened in 5.1.24
In specific this changelog.
Incompatible Change: The utf8_general_ci and ucs2_general_ci collations did not sort the letter “U+00DF SHARP S” equal to ‘s’.
As a result of this bug fix, indexes must be rebuilt for columns that use the utf8_general_ci or ucs2_general_ci collation for columns that contain SHARP S. See Section 2.13.3, “Checking Whether Tables or Indexes Must Be Rebuilt”. (Bug #27877)
Ensure you understand what this means and whether or not you want to use these charsets or whether you want to use the Percona compatible ones.
This percona blog post mentions the compatibility patches introduced in 5.1.58 by percona: