Q: my 16gb iPad mini 2 only has 11.6 gb of free storage, while iPad 3 has 13.x gb of free storage.

All models which are the same will have the same space available. However, depending on how you use it and any possible corrupted files, your own free space could vary. To get it back like all others, and to get rid of any possible corrupted files, you should reset your iPad back to its original factory condition. Then you can see how the empty space compares to all the others. But, be sure you do your backups, first.

Choosing an iOS Backup Method (Should I Use iTunes or iCloud to back up ...)

https://support.apple.com/kb/HT5262

Back up and Restore your iOS Device with iCloud or iTunes

http://support.apple.com/kb/ht1766

iTunes: About iOS Backups

http://support.apple.com/kb/ht4946

iOS: Troubleshooting Encrypted Backups

http://support.apple.com/kb/TS5162

Use iTunes to Restore your iOS Device to Factory Settings

http://support.apple.com/kb/ht1414