I feel sorry for you posting this during the iPhone 6 rush. You're lucky if anyone else sees it!
I had this issue! The fix is annoying, but it worked for me.
You probably have at least one track that is not syncing for some reason. Here's how to find it:
1) Go to settings -> general -> Usage -> Music and delete all the music from your phone.
2) Reboot the phone. This is important because the state of the phone is messed up and only a reboot fixes it.
3) Connect the phone. In iTunes preferences, select "Manually manage music". Open the phone using the little arrow and click music. Select any music you see (cmd-a) and delete it.
4) Wait until it finishes, then disconnect the phone and reboot it again.
5) Reconnect, turn OFF manually manage music, and sync. Wait until the entire sync completes.
6) Look at the music on the phone again. Scroll down and you will probably find one or more tracks that are greyed out with a dotted circle in the left hand column. THESE ARE THE TRACKS FAILING TO SYNC. Remove them from your library.
7) Repeat steps 1 through 5 to reset everything. Sync again, and everything should be fine.
I know it's convoluted, but this is the only way to find out which tracks are messing up the sync. For me it was ONE track out of over 5000! But my phone and ipad sync great now and I was able to replace the (iTunes store downloaded, oddly!) track with a pirated copy off the Internet. (I paid for it already!)
