Bad assumption I think. I have 1399 apps in my itunes. I keep a few hundred on my iphone. I only want ipad apps on my ipad with only a few that are iphone only. It took me almost 2 hours to go through all of them and manually uncheck all the ones I didn't want.
What made it worse is that I had already downloaded about 50 ipad apps in itunes. The only way to know which ones were for the ipad in the app check/uncheck sync list was to manually go to the main app list where it shows you which are ipad native and write all the names of the ipad apps down. I was then able to find them in the app check/uncheck sync list.
Ideally I would like an option for ipads to only automatically sync new ipad apps. The apps i download for my iphone 95% of the time I will only want them on the iphone.
This is the first release of itunes for ipad so I am sure they will improve this over time... I sure hope so anyway.