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.
The way iTunes manages apps in general is garbage.
The appstore setup is garbage to. How about wishlists, shopping lists, friends so that you can see what they bought and how they rated it.
Two years since this thread was last updated. iTunes 11 has just been released, and I have an iPad4 along with my old iPhone 3GS. Added videos to watch on the bigger iPad screen... and next thing I know, after a very long sync, it's on my iPhone too and the whole phone is slowed down.
I read Apple earned $20bn in the last quarter of 2010, but perhaps they still can't afford to pay someone with the skills to get this right.