You can still specify Apps which you do not want on your iPad in iTunes 11.
If you select from the View menu, Show Sidebar, the appearance is much like what you saw before.
If you select your iPad from the Sidebar Devices and press the Apps tab then:
There is a button by each installed App which says Remove. If you click that it will change to Will Remove and that App will be removed at the next sync.
For each App which has is not currently on your iPad the button will say Install. Click that and it will change the button to Will Install and that App will be installed at the next sync.
Wait a second. So I tried that but all the ones that I deleted from my iPad already had the option to Install instead of Remove. I thought if I didn't click Install, they would not install. However, they all tried to install even with that setting the way it was. Was I supposed to click Install for each one I DIDN'T want? If so, that's really counter-intuitive.