As a new owner of an iPad, I'm certainly not an expert, but I went through this trying to get my iPhone contacts into my iPad. I ended up with some contacts being duplicated up to 10 times!
If I remember correctly, if you uncheck the sync contacts box in iTunes, you will be asked if you want all contacts removed from you device.
I have also downloaded an app called ContactsBckp. In the settings of this app (you have to scroll up to see it) there is a remove all contacts option. When you have your contacts all sorted out, this is also a really easy way to keep them backed up.
Another useful app I use to keep my iPhone and iPad contacts the same is called iDrive. You can use this to restore from another device (after deleting all contacts using ContactsBackp).
It may sound complicated, but I have found using these two apps easy and quick, and I have peace of mind knowing I will never have to go through all that mess again.
Not sure if this will help but, when I set up my iPad I had it syncing contacts with icloud and my @me.com account. This caused me to have all my entries doubled. One from each account. Setting to only sync with one cleared it up.
Thanks for the help Tallahassee Lassie & Tyger_purr.
By (many) trial and error I discovered a work-around to deleting ALL contacts from my ipad!
On the iPad go to Settings > iCloud > Contacts - and turn on your contacts.
This causes a popup box called "Merge Contacts". If you proceed with this, it syncs your contacts with iCloud.
Next, go back to Contacts and turn the option OFF. Again, a popup box will appear that begins with "Turn Off Contacts". Then it asks you "What would you like to do with the previously synced iCloud contacts on your iPad?"
Two choices - Keep on my iPad or Delete from my iPad.
If you select Delete... then they will all be removed.
In the trial and error phase, I did this then tried turning the contacts back on but it just puts all those contacts back on my iPad. After doing this a couple of times I discovered I had to go to iCloud.com, login with my Apple ID (email and password), and edit all the contacts right there (ONE.AT.A.TIME).
THEN when I turned my iPad back on, it downloaded all of the edited contacts.
I think iCloud is way overrated and am thinking of doing away with it altogether. Too much trouble.
Don't know if you have this solved but i had the same problem.
I ended up logging into icloud, went to the contacts there and there you can select them all with the old control-a feature. then hit delete and gone they are. Hope that helps!