I suspect that your storage capacity is being taken up by "other". You can verify this by looking at the capacity bar in iTunes when your iPad is connected to your computer. "other" is basically all non media content like app data and documents, Safari History and bookmarks, Notes, Calendar entries, text messages, email messages, contacts and so on.
If the "other" is taking up a huge amount of space, something is corrupt on your iPad. Restoring the iPad may be necessary to make this right. Sometimes the only cure is to restore to factory settings and then rebuild your iPad by adding the content back onto it - not be restoring from a backup. Sometimes restoring from a backup can help this situation as well. You may have to experiment and see what works.
You can read this as well and see if recalibrating how the storage is calculated helps.
http://appchronicles.com/04/too-much-valuable-space-taken-up-by-other-category-h eres-how-to-fix-that/
Try the tips in the articles first, restore from a backup if that doesn't work, and restore to factory settings if nothing else does the trick.
How to backup and restore from a backup
http://support.apple.com/kb/HT1766