The complaint is that when you go to select what applications you want on your iPad (or iPhone, or iPod) they are all listed in one long list and you have to check (or uncheck) each app.
Personally, since you only have to do this once, and iPad-only apps won't sync anywhere else, I don't really see the hardship.
Besides, if you discover you've accidentally synced an unwanted iPhone app to your iPad, all you have to do is delete it off the iPad and iTunes will remember that for you.