This issue was first discovered with the SCORM reports having slow page load times and the fix turned out to be a general performance increase for Moodle. We have about 40,000 Moodle users and our basic and interactions SCORM reports span hundreds of pages.

It turns out that the call to array_shift in function emulate_bound_params from the file lib/dml/mysqli_native_moodle_database.php is very slow when it needs to evaluate thousands of bound query parameters.
The function array_shift reindexes the array which is not necessary for the function emulate_bound_params, and is at least one reason for the bad performance.

Our fix involves using array_reverse and array_pop for faster bound parameter evaluations. These are the before and after stats for a SCORM report page load time:
Pre-patch page load time: 128.496265 secs
Post-patch page load time: 5.149125 secs

We only made the fix for mysqli.

Please take a look at these branches at http://github.com/timgus/moodle for the patch and unit tests (for M23 and up):
array_shift_fix_m22
array_shift_fix_m23
array_shift_fix_m24
array_shift_fix_m25
array_shift_fix_master

I've attached my xhprof run before and after the fix when viewing a SCORM report page.