After a bit of thought, I've come up with a way for you to migrate to playlists with far less effort than setting up and maintaining two libraries/computers will take.
In iTunes create two normal playlists. One for the iPad, and one for the iPhone.
Now go to the Files Menu and create a Smart Play list. Set it up as Checked is true.
With the Checked playlist selected, go to the Edit menu and choose Select All.
Now drag the content to your other two playlists (see alternate option for smaller device)
At this point you now have two playlists that contain all your checked songs.
In the playlist for the device that you want to have fewer songs, remove the songs you don't want.
Alternately you could go to the the Checked playlist and start unchecking songs, then drag the results into the lesser-sized playlist (rather than the entire list and then deleting.
Now you have two playlists, one for each device, and you've done about the minimum amount of work possible to make them different. All that is left is plugging each device into iTunes, going to the Music sync tab and changing the settings to sync the right playlist for that device.
From that point on maintaining the playlists is simply a matter of removing and adding content. If you use the sorting and selection tools you can probably do this faster than checking/unchecking every single song.